rs7738656

Positions:

• chr6-121393702-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;