3-23993497-G-C

Variant names:

• chr3-23993497-G-C
• rs6550826

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 0.609 in 151,184 control chromosomes in the GnomAD database, including 28,621 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 0.61 (28621 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.684 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: 0.609 AC: 92061 AN: 151068 Hom.: 28599 Cov.: 30

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.609 AC: 92127 AN: 151184 Hom.: 28621 Cov.: 30 AF XY: 0.606 AC XY: 44765 AN XY: 73830

African (AFR) AF: 0.483 AC: 19880 AN: 41190

American (AMR) AF: 0.633 AC: 9630 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2456 AN: 3458

East Asian (EAS) AF: 0.482 AC: 2477 AN: 5136

South Asian (SAS) AF: 0.607 AC: 2916 AN: 4802

European-Finnish (FIN) AF: 0.594 AC: 6150 AN: 10362

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.689 AC: 46649 AN: 67712

Other (OTH) AF: 0.626 AC: 1317 AN: 2104

Alfa AF: 0.639 Hom.: 3875

Bravo AF: 0.607

Asia WGS AF: 0.548 AC: 1907 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	0.49
DANN	Benign	0.48
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6550826; hg19: chr3-24034988;