rs1891948

Variant names:

• chr13-53065010-G-A
• rs1891948

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.451 in 152,064 control chromosomes in the GnomAD database, including 15,714 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 0.45 (15714 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 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: 0.451 AC: 68458 AN: 151946 Hom.: 15689 Cov.: 33

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.451 AC: 68529 AN: 152064 Hom.: 15714 Cov.: 33 AF XY: 0.454 AC XY: 33761 AN XY: 74328

African (AFR) AF: 0.473 AC: 19610 AN: 41478

American (AMR) AF: 0.484 AC: 7404 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1622 AN: 3466

East Asian (EAS) AF: 0.632 AC: 3261 AN: 5162

South Asian (SAS) AF: 0.537 AC: 2586 AN: 4818

European-Finnish (FIN) AF: 0.415 AC: 4387 AN: 10564

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28174 AN: 67974

Other (OTH) AF: 0.479 AC: 1008 AN: 2106

Alfa AF: 0.432 Hom.: 24272

Bravo AF: 0.456

Asia WGS AF: 0.556 AC: 1931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	5.5
DANN	Benign	0.68
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1891948; hg19: chr13-53639145;