rs1925265

Variant names:

• chr10-117845427-A-G
• rs1925265

Your query was ambiguous. Multiple possible variants found:

• chr10-117845427-A-G
• chr10-117845427-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 0.377 in 152,032 control chromosomes in the GnomAD database, including 11,042 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 0.38 (11042 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 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: 0.377 AC: 57308 AN: 151914 Hom.: 11030 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.377 AC: 57352 AN: 152032 Hom.: 11042 Cov.: 32 AF XY: 0.374 AC XY: 27770 AN XY: 74332

African (AFR) AF: 0.337 AC: 13958 AN: 41458

American (AMR) AF: 0.358 AC: 5475 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1042 AN: 3466

East Asian (EAS) AF: 0.187 AC: 968 AN: 5170

South Asian (SAS) AF: 0.359 AC: 1726 AN: 4814

European-Finnish (FIN) AF: 0.392 AC: 4140 AN: 10554

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28682 AN: 67982

Other (OTH) AF: 0.360 AC: 759 AN: 2110

Alfa AF: 0.406 Hom.: 44354

Bravo AF: 0.375

Asia WGS AF: 0.337 AC: 1173 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	8.0
DANN	Benign	0.41
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1925265; hg19: chr10-119604938;