rs2149434

Variant names:

• chr13-46904209-A-C
• rs2149434

Your query was ambiguous. Multiple possible variants found:

• chr13-46904209-A-C
• chr13-46904209-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 0.562 in 152,010 control chromosomes in the GnomAD database, including 24,085 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 0.56 (24085 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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: 0.562 AC: 85363 AN: 151892 Hom.: 24071 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.562 AC: 85408 AN: 152010 Hom.: 24085 Cov.: 32 AF XY: 0.561 AC XY: 41717 AN XY: 74306

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.561

Alfa AF: 0.577 Hom.: 23105

Bravo AF: 0.561

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2149434; hg19: chr13-47478344;