10-37563459-A-G

Position:

• chr10-37563459-A-G

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 0.673 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.679

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6482044; hg19: chr10-37852387;