rs4903707

Variant names:

• chr14-40370665-A-G
• rs4903707
• ENST00000553464.2:n.501-15587A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-40370665-A-G
• chr14-40370665-A-T

Variant summary

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

The ENST00000553464.2(ENSG00000258526):​n.501-15587A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 151,836 control chromosomes in the GnomAD database, including 48,314 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 0.79 (48314 hom., cov: 32)
• Consequence: ENSG00000258526 ENST00000553464.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 2 publications found

Genes affected

ENSG00000258526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553464.2. 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
	ENSG00000258526	ENST00000553464.2	TSL:5	n.501-15587A>G		intron	N/A
	ENSG00000258526	ENST00000652126.1		n.643-856A>G		intron	N/A
	ENSG00000258526	ENST00000663500.1		n.481-15587A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119319 AN: 151720 Hom.: 48304 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.836

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.786 AC: 119374 AN: 151836 Hom.: 48314 Cov.: 32 AF XY: 0.792 AC XY: 58761 AN XY: 74214

African (AFR) AF: 0.576 AC: 23851 AN: 41428

American (AMR) AF: 0.876 AC: 13346 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3012 AN: 3472

East Asian (EAS) AF: 0.942 AC: 4881 AN: 5180

South Asian (SAS) AF: 0.777 AC: 3746 AN: 4824

European-Finnish (FIN) AF: 0.910 AC: 9631 AN: 10586

Middle Eastern (MID) AF: 0.843 AC: 241 AN: 286

European-Non Finnish (NFE) AF: 0.858 AC: 58193 AN: 67804

Other (OTH) AF: 0.805 AC: 1701 AN: 2114

Alfa AF: 0.832 Hom.: 23686

Bravo AF: 0.777

Asia WGS AF: 0.814 AC: 2798 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.51
DANN	Benign	0.57
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4903707; hg19: chr14-40839869;