rs10508887

Variant names:

• chr10-44700093-C-T
• rs10508887

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 0.0784 in 152,186 control chromosomes in the GnomAD database, including 1,237 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 0.078 (1237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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: 0.0783 AC: 11908 AN: 152068 Hom.: 1233 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0379

Gnomad ASJ AF: 0.0279

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.00301

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00235

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0784 AC: 11933 AN: 152186 Hom.: 1237 Cov.: 32 AF XY: 0.0767 AC XY: 5708 AN XY: 74410

African (AFR) AF: 0.233 AC: 9667 AN: 41494

American (AMR) AF: 0.0378 AC: 578 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0279 AC: 97 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1103 AN: 5146

South Asian (SAS) AF: 0.0317 AC: 153 AN: 4822

European-Finnish (FIN) AF: 0.00301 AC: 32 AN: 10618

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00235 AC: 160 AN: 68014

Other (OTH) AF: 0.0634 AC: 134 AN: 2114

Alfa AF: 0.0610 Hom.: 130

Bravo AF: 0.0889

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.73
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs10508887; hg19: chr10-45195541;