22-23888628-G-A

Variant names:

• chr22-23888628-G-A
• rs1984309
• ENST00000433835.3:c.432-6144G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433835.3(ENSG00000251357):​c.432-6144G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,108 control chromosomes in the GnomAD database, including 44,634 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 0.76 (44634 hom., cov: 31)
• Consequence: ENSG00000251357 ENST00000433835.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 6 publications found

Genes affected

ENSG00000251357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433835.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251357	ENST00000433835.3	TSL:5	c.432-6144G>A		intron	N/A	ENSP00000400325.3

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116059 AN: 151990 Hom.: 44578 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.764 AC: 116174 AN: 152108 Hom.: 44634 Cov.: 31 AF XY: 0.768 AC XY: 57107 AN XY: 74346

African (AFR) AF: 0.849 AC: 35239 AN: 41500

American (AMR) AF: 0.805 AC: 12301 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2449 AN: 3468

East Asian (EAS) AF: 0.649 AC: 3351 AN: 5162

South Asian (SAS) AF: 0.713 AC: 3439 AN: 4822

European-Finnish (FIN) AF: 0.782 AC: 8279 AN: 10582

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48558 AN: 67980

Other (OTH) AF: 0.746 AC: 1572 AN: 2106

Alfa AF: 0.750 Hom.: 6088

Bravo AF: 0.770

Asia WGS AF: 0.708 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.21
PhyloP100		-2.4

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

Other links and lift over

dbSNP: rs1984309; hg19: chr22-24230815;