rs2325406

Variant names:

• chr13-71270563-C-A
• rs2325406

Your query was ambiguous. Multiple possible variants found:

• chr13-71270563-C-A
• chr13-71270563-C-T

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 0.103 in 151,944 control chromosomes in the GnomAD database, including 1,049 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 0.10 (1049 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 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: 0.103 AC: 15599 AN: 151826 Hom.: 1050 Cov.: 32

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0765

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.0566

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.103 AC: 15599 AN: 151944 Hom.: 1049 Cov.: 32 AF XY: 0.100 AC XY: 7442 AN XY: 74272

African (AFR) AF: 0.0259 AC: 1076 AN: 41492

American (AMR) AF: 0.0764 AC: 1167 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3464

East Asian (EAS) AF: 0.164 AC: 846 AN: 5168

South Asian (SAS) AF: 0.0573 AC: 276 AN: 4818

European-Finnish (FIN) AF: 0.126 AC: 1330 AN: 10552

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10187 AN: 67872

Other (OTH) AF: 0.107 AC: 225 AN: 2108

Alfa AF: 0.125 Hom.: 833

Bravo AF: 0.0966

Asia WGS AF: 0.0830 AC: 286 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs2325406; hg19: chr13-71844695;