chr2-102310626-G-A

Position:

• chr2-102310626-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 0.479 in 151,822 control chromosomes in the GnomAD database, including 17,666 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 0.48 (17666 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72604 AN: 151704 Hom.: 17647 Cov.: 30

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.479 AC: 72654 AN: 151822 Hom.: 17666 Cov.: 30 AF XY: 0.475 AC XY: 35257 AN XY: 74188

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.516

Alfa AF: 0.504 Hom.: 2799

Bravo AF: 0.466

Asia WGS AF: 0.503 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.69
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11685480; hg19: chr2-102927086; COSMIC: COSV52113548;