rs689683

chr7-138312974-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;