rs2405414

Variant names:

• chr13-46542816-G-A
• rs2405414

Your query was ambiguous. Multiple possible variants found:

• chr13-46542816-G-A
• chr13-46542816-G-C

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 0.352 in 151,982 control chromosomes in the GnomAD database, including 11,620 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 0.35 (11620 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.352 AC: 53494 AN: 151864 Hom.: 11612 Cov.: 32

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.352 AC: 53511 AN: 151982 Hom.: 11620 Cov.: 32 AF XY: 0.359 AC XY: 26677 AN XY: 74284

African (AFR) AF: 0.0837 AC: 3472 AN: 41478

American (AMR) AF: 0.437 AC: 6676 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3464

East Asian (EAS) AF: 0.379 AC: 1960 AN: 5168

South Asian (SAS) AF: 0.444 AC: 2142 AN: 4822

European-Finnish (FIN) AF: 0.543 AC: 5719 AN: 10534

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30727 AN: 67934

Other (OTH) AF: 0.372 AC: 784 AN: 2110

Alfa AF: 0.390 Hom.: 2149

Bravo AF: 0.330

Asia WGS AF: 0.373 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2405414; hg19: chr13-47116951;