22-24668842-C-T

Variant names:

• chr22-24668842-C-T
• rs131464

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 0.25 in 151,968 control chromosomes in the GnomAD database, including 6,018 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 0.25 (6018 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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: 0.250 AC: 37968 AN: 151850 Hom.: 6011 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.250 AC: 37985 AN: 151968 Hom.: 6018 Cov.: 31 AF XY: 0.263 AC XY: 19520 AN XY: 74266

African (AFR) AF: 0.104 AC: 4325 AN: 41484

American (AMR) AF: 0.449 AC: 6858 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3468

East Asian (EAS) AF: 0.558 AC: 2856 AN: 5120

South Asian (SAS) AF: 0.370 AC: 1787 AN: 4828

European-Finnish (FIN) AF: 0.340 AC: 3584 AN: 10546

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16972 AN: 67950

Other (OTH) AF: 0.265 AC: 558 AN: 2104

Alfa AF: 0.264 Hom.: 4503

Bravo AF: 0.254

Asia WGS AF: 0.409 AC: 1422 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.76
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs131464; hg19: chr22-25064809;