rs1245911

Variant names:

• chr10-109773251-A-C
• rs1245911

Your query was ambiguous. Multiple possible variants found:

• chr10-109773251-A-C
• chr10-109773251-A-G
• chr10-109773251-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 0.529 in 151,992 control chromosomes in the GnomAD database, including 22,357 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 0.53 (22357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.717 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: 0.529 AC: 80363 AN: 151874 Hom.: 22303 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.529 AC: 80479 AN: 151992 Hom.: 22357 Cov.: 32 AF XY: 0.538 AC XY: 39942 AN XY: 74278

African (AFR) AF: 0.650 AC: 26964 AN: 41460

American (AMR) AF: 0.606 AC: 9251 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1616 AN: 3468

East Asian (EAS) AF: 0.736 AC: 3798 AN: 5162

South Asian (SAS) AF: 0.737 AC: 3545 AN: 4810

European-Finnish (FIN) AF: 0.439 AC: 4630 AN: 10556

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.428 AC: 29106 AN: 67950

Other (OTH) AF: 0.536 AC: 1132 AN: 2110

Alfa AF: 0.496 Hom.: 3450

Bravo AF: 0.543

Asia WGS AF: 0.764 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.57
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1245911; hg19: chr10-111533009;