Genetic Variant ENSG00000285163:n.739T>C (chr16-85947995-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000645383.1(ENSG00000285163):n.739T>C 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 0.754 in 152,220 control chromosomes in the GnomAD database, including 44,264 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 0.75 ( 44256 hom., cov: 33)

Exomes 𝑓: 0.77 ( 8 hom. )

Consequence

ENSG00000285163
ENST00000645383.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.41

Publications

5 publications found

Variant links:

Genes affected

ENSG00000285163 (HGNC:):

ENSG00000285163 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371388	XR_001752395.1 link	n.383T>C		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285163	ENST00000645383.1 link	n.739T>C	non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000285163	ENST00000646214.1 link	n.423T>C	non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000285163	ENST00000646986.2 link	n.1061T>C	non_coding_transcript_exon_variant	Exon 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.754

AC:

114625

AN:

152080

Hom.:

44190

Cov.:

show subpopulations

Gnomad AFR

AF:

0.895

Gnomad AMI

AF:

0.680

Gnomad AMR

AF:

0.731

Gnomad ASJ

AF:

0.600

Gnomad EAS

AF:

0.901

Gnomad SAS

AF:

0.782

Gnomad FIN

AF:

0.781

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.667

Gnomad OTH

AF:

0.686

GnomAD4 exome

AF:

0.773

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

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:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.833

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.775

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.754

AC:

114756

AN:

152198

Hom.:

44256

Cov.:

AF XY:

0.760

AC XY:

56518

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.896

AC:

37199

AN:

41538

American (AMR)

AF:

0.731

AC:

11182

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.600

AC:

2081

AN:

3470

East Asian (EAS)

AF:

0.902

AC:

4676

AN:

5186

South Asian (SAS)

AF:

0.783

AC:

3759

AN:

4802

European-Finnish (FIN)

AF:

0.781

AC:

8281

AN:

10600

Middle Eastern (MID)

AF:

0.534

AC:

157

AN:

294

European-Non Finnish (NFE)

AF:

0.667

AC:

45343

AN:

67986

Other (OTH)

AF:

0.690

AC:

1459

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1382

2765

4147

5530

6912

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<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:

0.707

Hom.:

52053

Bravo

AF:

0.756

Asia WGS

AF:

0.855

AC:

2974

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.97

(source)

DANN

Benign

0.35

PhyloP100

-2.4

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