2-112852309-T-C

Variant names:

• chr2-112852309-T-C
• rs6735739

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 0.566 in 151,984 control chromosomes in the GnomAD database, including 25,364 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 0.57 (25364 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86095 AN: 151866 Hom.: 25367 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.566 AC: 86096 AN: 151984 Hom.: 25364 Cov.: 31 AF XY: 0.560 AC XY: 41568 AN XY: 74286

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.578

Alfa AF: 0.516 Hom.: 1674

Bravo AF: 0.556

Asia WGS AF: 0.448 AC: 1558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.7
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6735739; hg19: chr2-113609886;