2-117576666-C-T

Variant names:

• chr2-117576666-C-T
• rs1516003

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 0.501 in 152,004 control chromosomes in the GnomAD database, including 22,529 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 0.50 (22529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.991

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 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: 0.501 AC: 76156 AN: 151886 Hom.: 22526 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.501 AC: 76155 AN: 152004 Hom.: 22529 Cov.: 32 AF XY: 0.504 AC XY: 37473 AN XY: 74296

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.554

Alfa AF: 0.441 Hom.: 1514

Bravo AF: 0.478

Asia WGS AF: 0.538 AC: 1870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	19
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: rs1516003; hg19: chr2-118334242;