2-112846151-T-G

Position:

• chr2-112846151-T-G

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 0.594 in 152,108 control chromosomes in the GnomAD database, including 27,434 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 0.59 (27434 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 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: 0.594 AC: 90298 AN: 151990 Hom.: 27416 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.594 AC: 90343 AN: 152108 Hom.: 27434 Cov.: 33 AF XY: 0.586 AC XY: 43548 AN XY: 74362

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.595

Alfa AF: 0.640 Hom.: 39681

Bravo AF: 0.588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10169916; hg19: chr2-113603728;