rs2149266

Variant names:

• chr13-85783983-T-C
• rs2149266

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 0.454 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.600 AC: 24843 AN: 41426

American (AMR) AF: 0.281 AC: 4278 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3466

East Asian (EAS) AF: 0.0600 AC: 310 AN: 5168

South Asian (SAS) AF: 0.333 AC: 1604 AN: 4824

European-Finnish (FIN) AF: 0.614 AC: 6451 AN: 10514

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.427 AC: 29011 AN: 67886

Other (OTH) AF: 0.400 AC: 844 AN: 2112

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2149266; hg19: chr13-86358118;