Genetic Variant C16orf74:p.Ser20_Ser21del (chr16-85710272-GGCTGCT-G) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP3BP6_ModerateBS2

The NM_206967.3(C16orf74):c.58_63delAGCAGC(p.Ser20_Ser21del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00692 in 1,509,930 control chromosomes in the GnomAD database, including 46 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0048 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0071 ( 44 hom. )

Consequence

C16orf74
NM_206967.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.57

Publications

1 publications found

Variant links:

Genes affected

C16orf74 (HGNC:23362): (chromosome 16 open reading frame 74)

C16orf74 links:

ENSG00000287125 (HGNC:):

ENSG00000287125 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_206967.3

BP6

Variant 16-85710272-GGCTGCT-G is Benign according to our data. Variant chr16-85710272-GGCTGCT-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2646943.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_206967.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
C16orf74	NM_206967.3	MANE Select	c.58_63delAGCAGC	p.Ser20_Ser21del	conservative_inframe_deletion	Exon 3 of 4	NP_996850.1	Q96GX8-1
C16orf74	NR_161452.1		n.289_294delAGCAGC		non_coding_transcript_exon	Exon 4 of 5
C16orf74	NR_161454.1		n.225_230delAGCAGC		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
C16orf74	ENST00000284245.9	TSL:1 MANE Select	c.58_63delAGCAGC	p.Ser20_Ser21del	conservative_inframe_deletion	Exon 3 of 4	ENSP00000284245.3	Q96GX8-1
C16orf74	ENST00000602583.5	TSL:1	c.22_27delAGCAGC	p.Ser8_Ser9del	conservative_inframe_deletion	Exon 1 of 2	ENSP00000473536.1	Q96GX8-2
C16orf74	ENST00000602675.5	TSL:1	c.-84_-79delAGCAGC		5_prime_UTR	Exon 3 of 4	ENSP00000473306.1	R4GMV5

Frequencies

GnomAD3 genomes

AF:

0.00485

AC:

738

AN:

152106

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00179

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00884

Gnomad ASJ

AF:

0.00288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00579

Gnomad FIN

AF:

0.000566

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00687

Gnomad OTH

AF:

0.00862

GnomAD2 exomes

AF:

0.00435

AC:

483

AN:

111014

AF XY:

0.00443

show subpopulations

Gnomad AFR exome

AF:

0.000882

Gnomad AMR exome

AF:

0.00290

Gnomad ASJ exome

AF:

0.00256

Gnomad EAS exome

AF:

0.000188

Gnomad FIN exome

AF:

0.000263

Gnomad NFE exome

AF:

0.00636

Gnomad OTH exome

AF:

0.00385

GnomAD4 exome

AF:

0.00715

AC:

9707

AN:

1357706

Hom.:

AF XY:

0.00721

AC XY:

4841

AN XY:

671660

show subpopulations

African (AFR)

AF:

0.00127

AC:

AN:

27638

American (AMR)

AF:

0.00415

AC:

109

AN:

26266

Ashkenazi Jewish (ASJ)

AF:

0.00305

AC:

AN:

23608

East Asian (EAS)

AF:

0.0000932

AC:

AN:

32194

South Asian (SAS)

AF:

0.00498

AC:

355

AN:

71320

European-Finnish (FIN)

AF:

0.000898

AC:

AN:

44532

Middle Eastern (MID)

AF:

0.00813

AC:

AN:

5532

European-Non Finnish (NFE)

AF:

0.00812

AC:

8692

AN:

1070290

Other (OTH)

AF:

0.00632

AC:

356

AN:

56326

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.451

Heterozygous variant carriers

500

1001

1501

2002

2502

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

346

692

1038

1384

1730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00484

AC:

737

AN:

152224

Hom.:

Cov.:

AF XY:

0.00450

AC XY:

335

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.00178

AC:

AN:

41562

American (AMR)

AF:

0.00883

AC:

135

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00288

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5180

South Asian (SAS)

AF:

0.00580

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.000566

AC:

AN:

10592

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00686

AC:

466

AN:

67976

Other (OTH)

AF:

0.00853

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

105

140

175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00188

Hom.:

Bravo

AF:

0.00591

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.6

Mutation Taster

=264/36

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over