2-117443528-C-G

Position:

• chr2-117443528-C-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 0.0999 in 152,206 control chromosomes in the GnomAD database, including 1,412 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 0.10 (1412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 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: 0.0996 AC: 15153 AN: 152088 Hom.: 1395 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.00906

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0815

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

GnomAD4 genome AF: 0.0999 AC: 15199 AN: 152206 Hom.: 1412 Cov.: 32 AF XY: 0.0997 AC XY: 7422 AN XY: 74420

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.0970

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.00888

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0330

Gnomad4 OTH AF: 0.0806

Alfa AF: 0.0770 Hom.: 107

Bravo AF: 0.108

Asia WGS AF: 0.0810 AC: 283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2421930; hg19: chr2-118201104;