13-45872267-A-G

Variant names:

• chr13-45872267-A-G
• rs2254191

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 0.579 in 151,556 control chromosomes in the GnomAD database, including 27,084 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 0.58 (27084 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.784 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: 0.580 AC: 87758 AN: 151434 Hom.: 27087 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.579 AC: 87784 AN: 151556 Hom.: 27084 Cov.: 31 AF XY: 0.581 AC XY: 43034 AN XY: 74062

African (AFR) AF: 0.356 AC: 14732 AN: 41358

American (AMR) AF: 0.544 AC: 8295 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2094 AN: 3456

East Asian (EAS) AF: 0.805 AC: 4122 AN: 5122

South Asian (SAS) AF: 0.683 AC: 3283 AN: 4808

European-Finnish (FIN) AF: 0.694 AC: 7267 AN: 10472

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46064 AN: 67782

Other (OTH) AF: 0.595 AC: 1254 AN: 2108

Alfa AF: 0.637 Hom.: 39000

Bravo AF: 0.559

Asia WGS AF: 0.725 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0040
DANN	Benign	0.23
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs2254191; hg19: chr13-46446402; COSMIC: COSV69348897;