rs689683

Variant names:

• chr7-138312974-T-C
• rs689683

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.542 in 151,760 control chromosomes in the GnomAD database, including 23,083 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 0.54 (23083 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82163 AN: 151642 Hom.: 23074 Cov.: 30

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.552

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.542 AC: 82200 AN: 151760 Hom.: 23083 Cov.: 30 AF XY: 0.540 AC XY: 40011 AN XY: 74148

African (AFR) AF: 0.421 AC: 17409 AN: 41366

American (AMR) AF: 0.491 AC: 7482 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2279 AN: 3470

East Asian (EAS) AF: 0.328 AC: 1681 AN: 5126

South Asian (SAS) AF: 0.597 AC: 2867 AN: 4806

European-Finnish (FIN) AF: 0.596 AC: 6284 AN: 10538

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42260 AN: 67914

Other (OTH) AF: 0.549 AC: 1154 AN: 2102

Alfa AF: 0.571 Hom.: 3089

Bravo AF: 0.525

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.076
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs689683; hg19: chr7-137997719;