rs1894758

Variant names:

• chr13-111390948-G-A
• rs1894758

Your query was ambiguous. Multiple possible variants found:

• chr13-111390948-G-A
• chr13-111390948-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 0.242 in 152,136 control chromosomes in the GnomAD database, including 5,670 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 0.24 (5670 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.589
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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: 0.242 AC: 36806 AN: 152018 Hom.: 5658 Cov.: 33

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.242 AC: 36832 AN: 152136 Hom.: 5670 Cov.: 33 AF XY: 0.248 AC XY: 18442 AN XY: 74366

African (AFR) AF: 0.0983 AC: 4084 AN: 41526

American (AMR) AF: 0.355 AC: 5430 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1181 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3627 AN: 5156

South Asian (SAS) AF: 0.401 AC: 1932 AN: 4820

European-Finnish (FIN) AF: 0.236 AC: 2501 AN: 10594

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17293 AN: 67974

Other (OTH) AF: 0.266 AC: 562 AN: 2112

Alfa AF: 0.240 Hom.: 5859

Bravo AF: 0.247

Asia WGS AF: 0.516 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.40
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1894758; hg19: chr13-112043295; COSMIC: COSV62100321;