rs13418717

chr2-126905321-T-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;