rs10887701

Variant names:

• chr10-80260813-C-T
• rs10887701

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 0.425 in 152,044 control chromosomes in the GnomAD database, including 14,829 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 0.43 (14829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64625 AN: 151926 Hom.: 14822 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.425 AC: 64657 AN: 152044 Hom.: 14829 Cov.: 32 AF XY: 0.434 AC XY: 32210 AN XY: 74284

African (AFR) AF: 0.329 AC: 13631 AN: 41456

American (AMR) AF: 0.444 AC: 6794 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1416 AN: 3470

East Asian (EAS) AF: 0.961 AC: 4953 AN: 5156

South Asian (SAS) AF: 0.520 AC: 2507 AN: 4822

European-Finnish (FIN) AF: 0.497 AC: 5252 AN: 10578

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28556 AN: 67962

Other (OTH) AF: 0.454 AC: 957 AN: 2110

Alfa AF: 0.425 Hom.: 44027

Bravo AF: 0.423

Asia WGS AF: 0.672 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.53
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs10887701; hg19: chr10-82020569;