chr2-112496-A-C

Position:

• chr2-112496-A-C

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 0.81 in 152,094 control chromosomes in the GnomAD database, including 50,070 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 0.81 (50070 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.810 AC: 123074 AN: 151976 Hom.: 50039 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.810 AC: 123150 AN: 152094 Hom.: 50070 Cov.: 32 AF XY: 0.809 AC XY: 60141 AN XY: 74338

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.783

Alfa AF: 0.813 Hom.: 61169

Bravo AF: 0.797

Asia WGS AF: 0.746 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs300774; hg19: chr2-112496;