rs7738656

Variant names:

• chr6-121393702-G-A
• rs7738656

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 0.232 in 151,888 control chromosomes in the GnomAD database, including 4,696 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 0.23 (4696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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: 0.231 AC: 35131 AN: 151770 Hom.: 4685 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.232 AC: 35189 AN: 151888 Hom.: 4696 Cov.: 32 AF XY: 0.237 AC XY: 17587 AN XY: 74204

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.201

Alfa AF: 0.177 Hom.: 5490

Bravo AF: 0.251

Asia WGS AF: 0.284 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7738656; hg19: chr6-121714848; COSMIC: COSV74180850;