22-23953099-T-C

Position:

• chr22-23953099-T-C

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 0.576 in 147,752 control chromosomes in the GnomAD database, including 23,139 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 0.58 (23139 hom., cov: 44)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23953099T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231271	ENST00000440099.1	n.134-788T>C		intron_variant		6
ENSG00000290199	ENST00000703580.1	n.309+20669A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.576 AC: 85049 AN: 147638 Hom.: 23116 Cov.: 44

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.576 AC: 85113 AN: 147752 Hom.: 23139 Cov.: 44 AF XY: 0.581 AC XY: 41902 AN XY: 72124

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.578

Alfa AF: 0.582 Hom.: 2751

Asia WGS AF: 0.505 AC: 1688 AN: 3346

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2739330; hg19: chr22-24295286;