2-117174661-C-T

Position:

• chr2-117174661-C-T

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 0.49 in 151,998 control chromosomes in the GnomAD database, including 20,997 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 0.49 (20997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74437 AN: 151880 Hom.: 20986 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.490 AC: 74469 AN: 151998 Hom.: 20997 Cov.: 32 AF XY: 0.501 AC XY: 37226 AN XY: 74298

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.531

Alfa AF: 0.546 Hom.: 8661

Bravo AF: 0.485

Asia WGS AF: 0.682 AC: 2368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs729253; hg19: chr2-117932237;