chr2-117716440-C-T

Variant names:

• chr2-117716440-C-T
• rs4849613

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0506 AC: 2102 AN: 41556

American (AMR) AF: 0.111 AC: 1697 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3470

East Asian (EAS) AF: 0.112 AC: 579 AN: 5186

South Asian (SAS) AF: 0.138 AC: 666 AN: 4828

European-Finnish (FIN) AF: 0.110 AC: 1169 AN: 10600

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7937 AN: 68028

Other (OTH) AF: 0.0852 AC: 180 AN: 2112

Alfa AF: 0.103 Hom.: 1674

Bravo AF: 0.0914

Asia WGS AF: 0.129 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.065
DANN	Benign	0.42
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs4849613; hg19: chr2-118474016;