chr22-24668567-T-C

Variant names:

• chr22-24668567-T-C
• rs140344

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 0.62 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.763 AC: 30670 AN: 40210

American (AMR) AF: 0.687 AC: 10458 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3468

East Asian (EAS) AF: 0.773 AC: 3974 AN: 5142

South Asian (SAS) AF: 0.719 AC: 3421 AN: 4760

European-Finnish (FIN) AF: 0.509 AC: 5372 AN: 10564

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35602 AN: 67880

Other (OTH) AF: 0.615 AC: 1288 AN: 2096

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
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs140344; hg19: chr22-25064534;