22-24668567-T-C

Variant names:

• chr22-24668567-T-C
• rs140344

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 0.62 in 150,552 control chromosomes in the GnomAD database, including 29,940 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 0.62 (29940 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.620 AC: 93210 AN: 150436 Hom.: 29887 Cov.: 28

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.620 AC: 93323 AN: 150552 Hom.: 29940 Cov.: 28 AF XY: 0.625 AC XY: 45958 AN XY: 73550

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.615

Alfa AF: 0.570 Hom.: 3544

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs140344; hg19: chr22-25064534;