3-24072206-T-C

Variant names:

• chr3-24072206-T-C
• rs6801153

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 0.736 in 152,006 control chromosomes in the GnomAD database, including 41,291 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 0.74 (41291 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.755 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: 0.736 AC: 111768 AN: 151888 Hom.: 41265 Cov.: 30

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.736 AC: 111847 AN: 152006 Hom.: 41291 Cov.: 30 AF XY: 0.733 AC XY: 54474 AN XY: 74284

African (AFR) AF: 0.733 AC: 30410 AN: 41464

American (AMR) AF: 0.635 AC: 9696 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2465 AN: 3472

East Asian (EAS) AF: 0.739 AC: 3801 AN: 5140

South Asian (SAS) AF: 0.672 AC: 3230 AN: 4806

European-Finnish (FIN) AF: 0.756 AC: 7982 AN: 10560

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51697 AN: 67984

Other (OTH) AF: 0.729 AC: 1535 AN: 2106

Alfa AF: 0.742 Hom.: 69960

Bravo AF: 0.727

Asia WGS AF: 0.716 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.31
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs6801153; hg19: chr3-24113697;