rs1040802

Variant names:

• chr6-62762537-A-C
• rs1040802

Your query was ambiguous. Multiple possible variants found:

• chr6-62762537-A-C
• chr6-62762537-A-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 0.448 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;