rs2254191

Positions:

• chr13-45872267-A-G
• chr13-45872267-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.595

Alfa AF: 0.652 Hom.: 30546

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

Splicing

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

Publications

LitVar

Other links and lift over

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