rs10510107

Variant names:

• chr10-122269956-A-G
• rs10510107

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 0.039 in 152,222 control chromosomes in the GnomAD database, including 330 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 0.039 (330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 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: 0.0390 AC: 5939 AN: 152104 Hom.: 330 Cov.: 32

Gnomad AFR AF: 0.00891

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.0311

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0253

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0390 AC: 5939 AN: 152222 Hom.: 330 Cov.: 32 AF XY: 0.0426 AC XY: 3171 AN XY: 74416

Gnomad4 AFR AF: 0.00888

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.0311

Gnomad4 NFE AF: 0.0253

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0535 Hom.: 108

Bravo AF: 0.0515

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.039
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510107; hg19: chr10-124029471;