dbSNP rs7849955: ENSG00000285082:c.141-45014G>A (chr9-117803051-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000697666.1(ENSG00000285082):c.141-45014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,044 control chromosomes in the GnomAD database, including 1,590 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 0.14 ( 1588 hom., cov: 32)

Exomes 𝑓: 0.075 ( 2 hom. )

Consequence

ENSG00000285082
ENST00000697666.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Publications

2 publications found

Variant links:

Genes affected

ENSG00000285082 (HGNC:):

ENSG00000285082 links:

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new If you want to explore the variant's impact on the transcript ENST00000697666.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697666.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
ENSG00000285082	ENST00000697666.1	c.141-45014G>A	intron	N/A	ENSP00000513391.1	A0A8V8TMK6
ENSG00000285082	ENST00000646089.2	c.94-45014G>A	intron	N/A	ENSP00000496197.1	A0A2R8YGN2
ENSG00000285082	ENST00000697637.1	c.94-45014G>A	intron	N/A	ENSP00000513367.1	A0A2R8YGN2

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20650

AN:

151820

Hom.:

1587

Cov.:

show subpopulations

Gnomad AFR

AF:

0.114

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.00233

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.0749

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.151

GnomAD4 exome

AF:

0.0755

AC:

AN:

106

Hom.:

Cov.:

AF XY:

0.0625

AC XY:

AN XY:

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

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:

0.0641

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.107

AC:

AN:

Other (OTH)

AC:

AN:

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00134009), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.338

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.136

AC:

20662

AN:

151938

Hom.:

1588

Cov.:

AF XY:

0.131

AC XY:

9705

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.114

AC:

4722

AN:

41482

American (AMR)

AF:

0.144

AC:

2189

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

893

AN:

3466

East Asian (EAS)

AF:

0.00233

AC:

AN:

5146

South Asian (SAS)

AF:

0.109

AC:

525

AN:

4824

European-Finnish (FIN)

AF:

0.0749

AC:

794

AN:

10606

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.164

AC:

11125

AN:

67878

Other (OTH)

AF:

0.151

AC:

318

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

912

1823

2735

3646

4558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<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:

0.140

Hom.:

907

Bravo

AF:

0.138

Asia WGS

AF:

0.0620

AC:

217

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.8

(source)

DANN

Benign

0.58

PhyloP100

-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over