chr3-96672116-C-T

Variant names:

• chr3-96672116-C-T
• rs1825828

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 0.685 in 151,582 control chromosomes in the GnomAD database, including 37,383 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 0.69 (37383 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103826 AN: 151468 Hom.: 37384 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.685 AC: 103850 AN: 151582 Hom.: 37383 Cov.: 31 AF XY: 0.686 AC XY: 50855 AN XY: 74108

African (AFR) AF: 0.433 AC: 17755 AN: 41004

American (AMR) AF: 0.709 AC: 10830 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2744 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3859 AN: 5134

South Asian (SAS) AF: 0.840 AC: 4046 AN: 4816

European-Finnish (FIN) AF: 0.745 AC: 7886 AN: 10582

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54271 AN: 67986

Other (OTH) AF: 0.736 AC: 1551 AN: 2106

Alfa AF: 0.716 Hom.: 5775

Bravo AF: 0.665

Asia WGS AF: 0.777 AC: 2701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.67
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1825828; hg19: chr3-96390960;