rs924033

Variant names:

• chr4-89514402-T-G
• rs924033
• ENST00000659714.1:n.546+22908T>G

Variant summary

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

The ENST00000659714.1(ENSG00000251095):​n.546+22908T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0539 in 152,220 control chromosomes in the GnomAD database, including 305 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 0.054 (305 hom., cov: 31)
• Consequence: ENSG00000251095 ENST00000659714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462

Genes affected

ENSG00000251095 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0828 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
ENSG00000251095	ENST00000659714.1	n.546+22908T>G		intron_variant	Intron 1 of 2
ENSG00000251095	ENST00000659878.1	n.360-73419T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0540 AC: 8214 AN: 152102 Hom.: 305 Cov.: 31

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0539 AC: 8212 AN: 152220 Hom.: 305 Cov.: 31 AF XY: 0.0525 AC XY: 3910 AN XY: 74422

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0319

Gnomad4 ASJ AF: 0.0257

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00602

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0728 Hom.: 259

Bravo AF: 0.0474

Asia WGS AF: 0.00751 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs924033; hg19: chr4-90435553;