rs10508997

Positions:

• chr10-53722881-A-G
• chr10-53722881-A-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 0.2 in 152,000 control chromosomes in the GnomAD database, including 4,253 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 0.20 (4253 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30413 AN: 151882 Hom.: 4243 Cov.: 32

Gnomad AFR AF: 0.0579

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.200 AC: 30433 AN: 152000 Hom.: 4253 Cov.: 32 AF XY: 0.207 AC XY: 15359 AN XY: 74270

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.203

Alfa AF: 0.210 Hom.: 492

Bravo AF: 0.200

Asia WGS AF: 0.457 AC: 1579 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508997; hg19: chr10-55482641;