22-24678896-G-T

Variant names:

• chr22-24678896-G-T
• rs6004233

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 0.503 in 151,742 control chromosomes in the GnomAD database, including 19,252 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 0.50 (19252 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.54 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: 0.503 AC: 76285 AN: 151624 Hom.: 19238 Cov.: 30

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.503 AC: 76341 AN: 151742 Hom.: 19252 Cov.: 30 AF XY: 0.504 AC XY: 37365 AN XY: 74122

African (AFR) AF: 0.526 AC: 21764 AN: 41404

American (AMR) AF: 0.546 AC: 8324 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3464

East Asian (EAS) AF: 0.465 AC: 2366 AN: 5088

South Asian (SAS) AF: 0.558 AC: 2681 AN: 4806

European-Finnish (FIN) AF: 0.449 AC: 4739 AN: 10556

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32866 AN: 67856

Other (OTH) AF: 0.513 AC: 1085 AN: 2114

Alfa AF: 0.478 Hom.: 2175

Bravo AF: 0.513

Asia WGS AF: 0.504 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.45
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs6004233; hg19: chr22-25074863;