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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.146

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508995; hg19: chr10-55137361;