rs13410476

Variant names:

• chr2-160554031-G-A
• rs13410476

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 0.372 in 151,770 control chromosomes in the GnomAD database, including 12,263 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 0.37 (12263 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 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: 0.371 AC: 56315 AN: 151650 Hom.: 12216 Cov.: 31

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.372 AC: 56428 AN: 151770 Hom.: 12263 Cov.: 31 AF XY: 0.372 AC XY: 27604 AN XY: 74184

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.346

Alfa AF: 0.280 Hom.: 7394

Bravo AF: 0.389

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13410476; hg19: chr2-161410542;