rs7739700

chr6-132633824-G-Achr6-132633824-G-T

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 0.339 in 151,988 control chromosomes in the GnomAD database, including 9,212 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 0.34 (9212 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 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: 0.339 AC: 51499 AN: 151872 Hom.: 9208 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.339 AC: 51533 AN: 151988 Hom.: 9212 Cov.: 31 AF XY: 0.341 AC XY: 25343 AN XY: 74274

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.329

Alfa AF: 0.272 Hom.: 1121

Bravo AF: 0.328

Asia WGS AF: 0.401 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.84
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7739700; hg19: chr6-132954963; COSMIC: COSV58605478;