chr10-45358501-T-A

Variant names:

• chr10-45358501-T-A
• rs7477350

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 0.676 in 151,966 control chromosomes in the GnomAD database, including 35,120 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 0.68 (35120 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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: 0.676 AC: 102702 AN: 151848 Hom.: 35079 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.676 AC: 102800 AN: 151966 Hom.: 35120 Cov.: 31 AF XY: 0.684 AC XY: 50816 AN XY: 74286

African (AFR) AF: 0.748 AC: 30994 AN: 41460

American (AMR) AF: 0.696 AC: 10628 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3468

East Asian (EAS) AF: 0.859 AC: 4434 AN: 5164

South Asian (SAS) AF: 0.594 AC: 2858 AN: 4810

European-Finnish (FIN) AF: 0.752 AC: 7942 AN: 10560

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41774 AN: 67920

Other (OTH) AF: 0.668 AC: 1410 AN: 2112

Alfa AF: 0.537 Hom.: 1492

Bravo AF: 0.678

Asia WGS AF: 0.723 AC: 2513 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.30
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs7477350; hg19: chr10-45853949;