rs2325406

Positions:

• chr13-71270563-C-A
• chr13-71270563-C-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 0.103 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0259

Gnomad4 AMR AF: 0.0764

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.0573

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.107

Alfa AF: 0.124 Hom.: 761

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2325406; hg19: chr13-71844695;