rs13410476

Variant names:

• chr2-160554031-G-A
• rs13410476

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 0.372 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.596 AC: 24641 AN: 41352

American (AMR) AF: 0.413 AC: 6294 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1231 AN: 5144

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4820

European-Finnish (FIN) AF: 0.300 AC: 3154 AN: 10530

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17223 AN: 67900

Other (OTH) AF: 0.346 AC: 729 AN: 2108

Alfa AF: 0.287 Hom.: 10132

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
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs13410476; hg19: chr2-161410542;