rs2149266

chr13-85783983-T-C

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 0.454 in 151,808 control chromosomes in the GnomAD database, including 17,104 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 (17104 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 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: 0.454 AC: 68800 AN: 151690 Hom.: 17074 Cov.: 31

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0598

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.454 AC: 68877 AN: 151808 Hom.: 17104 Cov.: 31 AF XY: 0.455 AC XY: 33719 AN XY: 74182

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0600

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.400

Alfa AF: 0.458 Hom.: 2057

Bravo AF: 0.432

Asia WGS AF: 0.238 AC: 826 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.54
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2149266; hg19: chr13-86358118;