rs13418717

Variant names:

• chr2-126905321-T-A
• rs13418717

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 0.0905 in 151,206 control chromosomes in the GnomAD database, including 1,033 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 0.090 (1033 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 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: 0.0904 AC: 13660 AN: 151092 Hom.: 1032 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0332

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0344

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.0905 AC: 13682 AN: 151206 Hom.: 1033 Cov.: 33 AF XY: 0.0906 AC XY: 6692 AN XY: 73876

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0332

Gnomad4 NFE AF: 0.0344

Gnomad4 OTH AF: 0.0826

Alfa AF: 0.0493 Hom.: 202

Bravo AF: 0.0980

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13418717; hg19: chr2-127662897;