Genetic Variant ENST00000562354.2:n.3224C>T (chr16-31711093-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000562354.2(ENSG00000290927):n.3224C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,120 control chromosomes in the GnomAD database, including 1,596 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 1595 hom., cov: 32)

Exomes 𝑓: 0.10 ( 1 hom. )

Consequence

ENSG00000290927
ENST00000562354.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0580

Publications

6 publications found

Variant links:

Genes affected

ENSG00000290927 (HGNC:):

ENSG00000290927 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290927	ENST00000562354.2 link	n.3224C>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
ENSG00000261731	ENST00000569175.2 link	n.240+652G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes

AF:

0.128

AC:

19372

AN:

151924

Hom.:

1592

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.0242

Gnomad AMR

AF:

0.0878

Gnomad ASJ

AF:

0.0533

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.331

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0755

Gnomad OTH

AF:

0.120

GnomAD4 exome

AF:

0.103

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0962

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0781

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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

GnomAD4 genome

AF:

0.128

AC:

19390

AN:

152042

Hom.:

1595

Cov.:

AF XY:

0.133

AC XY:

9849

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.194

AC:

8034

AN:

41442

American (AMR)

AF:

0.0876

AC:

1339

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0533

AC:

185

AN:

3470

East Asian (EAS)

AF:

0.257

AC:

1324

AN:

5160

South Asian (SAS)

AF:

0.330

AC:

1593

AN:

4822

European-Finnish (FIN)

AF:

0.140

AC:

1478

AN:

10564

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0755

AC:

5131

AN:

67986

Other (OTH)

AF:

0.125

AC:

264

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

814

1627

2441

3254

4068

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.0542

Hom.:

Bravo

AF:

0.122

Asia WGS

AF:

0.292

AC:

1010

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.3

(source)

DANN

Benign

0.51

PhyloP100

0.058

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over