rs10887710

Variant names:

• chr10-80270029-T-C
• rs10887710

Your query was ambiguous. Multiple possible variants found:

• chr10-80270029-T-C
• chr10-80270029-T-G

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 0.191 in 151,784 control chromosomes in the GnomAD database, including 3,166 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 0.19 (3166 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 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: 0.191 AC: 29017 AN: 151666 Hom.: 3172 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.191 AC: 29004 AN: 151784 Hom.: 3166 Cov.: 32 AF XY: 0.195 AC XY: 14435 AN XY: 74148

African (AFR) AF: 0.135 AC: 5582 AN: 41356

American (AMR) AF: 0.211 AC: 3214 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 742 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2642 AN: 5154

South Asian (SAS) AF: 0.199 AC: 956 AN: 4808

European-Finnish (FIN) AF: 0.251 AC: 2636 AN: 10512

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12524 AN: 67924

Other (OTH) AF: 0.211 AC: 444 AN: 2100

Alfa AF: 0.189 Hom.: 2772

Bravo AF: 0.189

Asia WGS AF: 0.304 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10887710; hg19: chr10-82029785;