2-112814780-T-C

Position:

• chr2-112814780-T-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 0.22 in 152,170 control chromosomes in the GnomAD database, including 3,980 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 0.22 (3980 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 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: 0.221 AC: 33530 AN: 152052 Hom.: 3981 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.220 AC: 33532 AN: 152170 Hom.: 3980 Cov.: 31 AF XY: 0.223 AC XY: 16593 AN XY: 74396

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.238

Alfa AF: 0.243 Hom.: 2245

Bravo AF: 0.212

Asia WGS AF: 0.190 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12469600; hg19: chr2-113572357;