rs1891760

Variant names:

• chr10-113499347-G-A
• rs1891760

Your query was ambiguous. Multiple possible variants found:

• chr10-113499347-G-A
• chr10-113499347-G-C

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 0.401 in 151,964 control chromosomes in the GnomAD database, including 13,307 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 0.40 (13307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 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: 0.401 AC: 60857 AN: 151846 Hom.: 13295 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.401 AC: 60886 AN: 151964 Hom.: 13307 Cov.: 31 AF XY: 0.413 AC XY: 30703 AN XY: 74266

African (AFR) AF: 0.230 AC: 9530 AN: 41448

American (AMR) AF: 0.546 AC: 8335 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3468

East Asian (EAS) AF: 0.553 AC: 2850 AN: 5158

South Asian (SAS) AF: 0.587 AC: 2824 AN: 4812

European-Finnish (FIN) AF: 0.532 AC: 5606 AN: 10528

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29096 AN: 67972

Other (OTH) AF: 0.389 AC: 820 AN: 2106

Alfa AF: 0.420 Hom.: 16011

Bravo AF: 0.393

Asia WGS AF: 0.562 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.5
DANN	Benign	0.55
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs1891760; hg19: chr10-115259106;