rs10508372

Variant names:

• chr10-8930055-G-A
• rs10508372

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 0.148 in 152,064 control chromosomes in the GnomAD database, including 2,752 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 0.15 (2752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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: 0.147 AC: 22382 AN: 151946 Hom.: 2742 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.0604

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.148 AC: 22432 AN: 152064 Hom.: 2752 Cov.: 32 AF XY: 0.154 AC XY: 11473 AN XY: 74334

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.0604

Gnomad4 NFE AF: 0.0697

Gnomad4 OTH AF: 0.166

Alfa AF: 0.0973 Hom.: 2410

Bravo AF: 0.161

Asia WGS AF: 0.433 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508372; hg19: chr10-8972018;