rs1317361

Variant names:

• chr10-89119547-A-G
• rs1317361

Your query was ambiguous. Multiple possible variants found:

• chr10-89119547-A-G
• chr10-89119547-A-T

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 0.386 in 152,068 control chromosomes in the GnomAD database, including 11,949 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 0.39 (11949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793
• Publications: 4 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 = 0.648 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: 0.386 AC: 58715 AN: 151950 Hom.: 11946 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.386 AC: 58734 AN: 152068 Hom.: 11949 Cov.: 32 AF XY: 0.392 AC XY: 29129 AN XY: 74308

African (AFR) AF: 0.270 AC: 11204 AN: 41464

American (AMR) AF: 0.388 AC: 5940 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3444 AN: 5166

South Asian (SAS) AF: 0.419 AC: 2019 AN: 4822

European-Finnish (FIN) AF: 0.483 AC: 5096 AN: 10554

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.416 AC: 28297 AN: 67996

Other (OTH) AF: 0.402 AC: 849 AN: 2110

Alfa AF: 0.406 Hom.: 40293

Bravo AF: 0.379

Asia WGS AF: 0.521 AC: 1811 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.70
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs1317361; hg19: chr10-90879304;