22-23893119-G-A

Position:

• chr22-23893119-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433835.3(ENSG00000251357):​c.432-1653G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,124 control chromosomes in the GnomAD database, including 2,615 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 0.18 (2615 hom., cov: 32)
• Consequence: ENSG00000251357 ENST00000433835.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606

Genes affected

ENSG00000251357 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23893119G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251357	ENST00000433835.3	c.432-1653G>A		intron_variant		5		ENSP00000400325.3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27558 AN: 152004 Hom.: 2609 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.181 AC: 27593 AN: 152124 Hom.: 2615 Cov.: 32 AF XY: 0.187 AC XY: 13888 AN XY: 74350

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.165

Alfa AF: 0.178 Hom.: 526

Bravo AF: 0.178

Asia WGS AF: 0.228 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4822445; hg19: chr22-24235306;