2-112807389-T-A

Position:

• chr2-112807389-T-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 0.311 in 150,684 control chromosomes in the GnomAD database, including 7,930 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 0.31 (7930 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 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: 0.311 AC: 46754 AN: 150576 Hom.: 7914 Cov.: 29

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.311 AC: 46792 AN: 150684 Hom.: 7930 Cov.: 29 AF XY: 0.319 AC XY: 23465 AN XY: 73532

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.320

Alfa AF: 0.137 Hom.: 265

Bravo AF: 0.313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7567619; hg19: chr2-113564966;