3-114205296-C-T

Variant names:

• chr3-114205296-C-T
• rs7611535

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 0.246 in 151,914 control chromosomes in the GnomAD database, including 4,956 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 0.25 (4956 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 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: 0.246 AC: 37382 AN: 151796 Hom.: 4950 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.246 AC: 37414 AN: 151914 Hom.: 4956 Cov.: 32 AF XY: 0.248 AC XY: 18425 AN XY: 74254

African (AFR) AF: 0.153 AC: 6314 AN: 41346

American (AMR) AF: 0.356 AC: 5442 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1265 AN: 5176

South Asian (SAS) AF: 0.220 AC: 1063 AN: 4822

European-Finnish (FIN) AF: 0.273 AC: 2893 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18798 AN: 67930

Other (OTH) AF: 0.252 AC: 532 AN: 2110

Alfa AF: 0.265 Hom.: 8014

Bravo AF: 0.251

Asia WGS AF: 0.224 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.054
DANN	Benign	0.21
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7611535; hg19: chr3-113924143;