rs7762370

Variant names:

• chr6-32432413-T-C
• rs7762370

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 0.0707 in 152,258 control chromosomes in the GnomAD database, including 546 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 0.071 (546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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: 0.0707 AC: 10752 AN: 152140 Hom.: 546 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0600

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0512

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0707 AC: 10767 AN: 152258 Hom.: 546 Cov.: 32 AF XY: 0.0681 AC XY: 5072 AN XY: 74450

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0213

Gnomad4 EAS AF: 0.00829

Gnomad4 SAS AF: 0.0594

Gnomad4 FIN AF: 0.0163

Gnomad4 NFE AF: 0.0512

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0619 Hom.: 114

Bravo AF: 0.0759

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7762370; hg19: chr6-32400190;