3-46115691-C-T

Variant names:

• chr3-46115691-C-T
• rs2131091

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 0.336 in 152,094 control chromosomes in the GnomAD database, including 10,564 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 0.34 (10564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 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: 0.336 AC: 51129 AN: 151976 Hom.: 10545 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.336 AC: 51162 AN: 152094 Hom.: 10564 Cov.: 32 AF XY: 0.342 AC XY: 25453 AN XY: 74346

African (AFR) AF: 0.0998 AC: 4144 AN: 41524

American (AMR) AF: 0.473 AC: 7231 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3468

East Asian (EAS) AF: 0.666 AC: 3431 AN: 5154

South Asian (SAS) AF: 0.371 AC: 1787 AN: 4818

European-Finnish (FIN) AF: 0.422 AC: 4469 AN: 10584

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27669 AN: 67956

Other (OTH) AF: 0.360 AC: 759 AN: 2110

Alfa AF: 0.361 Hom.: 1984

Bravo AF: 0.327

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2131091; hg19: chr3-46157183;