6-62762537-A-C

Position:

• chr6-62762537-A-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 0.448 in 151,906 control chromosomes in the GnomAD database, including 15,514 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 0.45 (15514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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 (NFE) allele frequency at 95% confidence interval = 0.49 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: 0.448 AC: 67960 AN: 151786 Hom.: 15512 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.448 AC: 67980 AN: 151906 Hom.: 15514 Cov.: 32 AF XY: 0.446 AC XY: 33126 AN XY: 74228

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.449

Alfa AF: 0.340 Hom.: 932

Bravo AF: 0.429

Asia WGS AF: 0.354 AC: 1233 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	7.5
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1040802; hg19: chr6-63472442;