rs10508995

Variant names:

• chr10-53377601-C-G
• rs10508995

Your query was ambiguous. Multiple possible variants found:

• chr10-53377601-C-G
• chr10-53377601-C-T

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 0.134 in 151,940 control chromosomes in the GnomAD database, including 1,705 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 0.13 (1705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.283 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: 0.134 AC: 20358 AN: 151822 Hom.: 1691 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.134 AC: 20410 AN: 151940 Hom.: 1705 Cov.: 32 AF XY: 0.141 AC XY: 10508 AN XY: 74276

African (AFR) AF: 0.114 AC: 4730 AN: 41364

American (AMR) AF: 0.267 AC: 4078 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3466

East Asian (EAS) AF: 0.171 AC: 883 AN: 5156

South Asian (SAS) AF: 0.296 AC: 1426 AN: 4816

European-Finnish (FIN) AF: 0.112 AC: 1182 AN: 10566

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7157 AN: 67984

Other (OTH) AF: 0.146 AC: 308 AN: 2114

Alfa AF: 0.0518 Hom.: 53

Bravo AF: 0.144

Asia WGS AF: 0.254 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.76
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs10508995; hg19: chr10-55137361;