rs689683

Variant names:

• chr7-138312974-T-C
• rs689683

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.549

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs689683; hg19: chr7-137997719;