chr22-23893116-G-C

Position:

• chr22-23893116-G-C

Variant summary

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

The ENST00000433835.3(ENSG00000251357):​c.432-1656G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,114 control chromosomes in the GnomAD database, including 3,135 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 0.20 (3135 hom., cov: 32)
• Consequence: ENSG00000251357 ENST00000433835.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

ENSG00000251357 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23893116G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251357	ENST00000433835.3	c.432-1656G>C		intron_variant		5		ENSP00000400325.3

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30034 AN: 151994 Hom.: 3126 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.198 AC: 30073 AN: 152114 Hom.: 3135 Cov.: 32 AF XY: 0.202 AC XY: 15046 AN XY: 74358

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.179

Alfa AF: 0.194 Hom.: 398

Bravo AF: 0.197

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.54

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: rs4822444; hg19: chr22-24235303;