chr2-117716440-C-T

Position:

• chr2-117716440-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 0.0968 in 152,294 control chromosomes in the GnomAD database, including 825 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 0.097 (825 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 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: 0.0967 AC: 14719 AN: 152176 Hom.: 825 Cov.: 33

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.0968 AC: 14737 AN: 152294 Hom.: 825 Cov.: 33 AF XY: 0.0977 AC XY: 7276 AN XY: 74466

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0852

Alfa AF: 0.109 Hom.: 1254

Bravo AF: 0.0914

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.065
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4849613; hg19: chr2-118474016;