rs1894756

Variant names:

• chr13-111366426-G-A
• rs1894756

Your query was ambiguous. Multiple possible variants found:

• chr13-111366426-G-A
• chr13-111366426-G-C
• chr13-111366426-G-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 0.227 in 152,078 control chromosomes in the GnomAD database, including 5,119 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 0.23 (5119 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 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: 0.227 AC: 34544 AN: 151960 Hom.: 5125 Cov.: 32

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.227 AC: 34530 AN: 152078 Hom.: 5119 Cov.: 32 AF XY: 0.229 AC XY: 16990 AN XY: 74342

African (AFR) AF: 0.0663 AC: 2754 AN: 41534

American (AMR) AF: 0.204 AC: 3117 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3470

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5186

South Asian (SAS) AF: 0.202 AC: 971 AN: 4806

European-Finnish (FIN) AF: 0.378 AC: 3982 AN: 10536

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21631 AN: 67960

Other (OTH) AF: 0.243 AC: 511 AN: 2106

Alfa AF: 0.287 Hom.: 29003

Bravo AF: 0.209

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.94
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1894756; hg19: chr13-112018773;