2-131413315-G-A

Position:

• chr2-131413315-G-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 0.523 in 152,038 control chromosomes in the GnomAD database, including 23,566 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 0.52 (23566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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: 0.523 AC: 79459 AN: 151922 Hom.: 23505 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.523 AC: 79576 AN: 152038 Hom.: 23566 Cov.: 32 AF XY: 0.528 AC XY: 39213 AN XY: 74306

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.538

Alfa AF: 0.412 Hom.: 15545

Bravo AF: 0.555

Asia WGS AF: 0.609 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7589111; hg19: chr2-132170888;