chr4-89514402-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000251095 (HGNC:53614):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659714.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251095	ENST00000659714.1		n.546+22908T>G		intron	N/A
	ENSG00000251095	ENST00000659878.1		n.360-73419T>G		intron	N/A
	ENSG00000251095	ENST00000776682.1		n.445-73419T>G		intron	N/A

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

African (AFR) AF: 0.0145 AC: 603 AN: 41554

American (AMR) AF: 0.0319 AC: 487 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0257 AC: 89 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00602 AC: 29 AN: 4818

European-Finnish (FIN) AF: 0.109 AC: 1154 AN: 10590

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0846 AC: 5754 AN: 68014

Other (OTH) AF: 0.0398 AC: 84 AN: 2110

Alfa AF: 0.0725 Hom.: 274

Bravo AF: 0.0474

Asia WGS AF: 0.00751 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs924033; hg19: chr4-90435553;