22-24678896-G-T

Variant names:

• chr22-24678896-G-T
• rs6004233

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.513

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6004233; hg19: chr22-25074863;