rs6482044

Variant names:

• chr10-37563459-A-G
• rs6482044

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.673 in 152,064 control chromosomes in the GnomAD database, including 34,639 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 0.67 (34639 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.796 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: 0.673 AC: 102270 AN: 151946 Hom.: 34628 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.673 AC: 102310 AN: 152064 Hom.: 34639 Cov.: 32 AF XY: 0.681 AC XY: 50625 AN XY: 74352

African (AFR) AF: 0.653 AC: 27078 AN: 41462

American (AMR) AF: 0.681 AC: 10397 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2466 AN: 3468

East Asian (EAS) AF: 0.609 AC: 3132 AN: 5144

South Asian (SAS) AF: 0.818 AC: 3939 AN: 4818

European-Finnish (FIN) AF: 0.774 AC: 8213 AN: 10610

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44875 AN: 67982

Other (OTH) AF: 0.679 AC: 1431 AN: 2108

Alfa AF: 0.676 Hom.: 5858

Bravo AF: 0.662

Asia WGS AF: 0.676 AC: 2349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6482044; hg19: chr10-37852387;