rs1984309

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr22-23888628-G-A
• chr22-23888628-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000251357 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000251357	ENST00000433835.3	c.432-6144G>A		intron_variant	Intron 4 of 5	5		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

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.746

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 v4.3

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

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: rs1984309; hg19: chr22-24230815;