chr17-4723059-A-C

Variant names:

• chr17-4723059-A-C
• rs4790694
• ENST00000786504.1:n.37+2954T>G

Variant summary

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

The ENST00000786504.1(ENSG00000302420):​n.37+2954T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 151,982 control chromosomes in the GnomAD database, including 43,420 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 0.74 (43420 hom., cov: 31)
• Consequence: ENSG00000302420 ENST00000786504.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 19 publications found

Genes affected

ENSG00000302420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 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
ENSG00000302420	ENST00000786504.1	n.37+2954T>G		intron_variant	Intron 1 of 1
ENSG00000302420	ENST00000786505.1	n.47-815T>G		intron_variant	Intron 1 of 3
ENSG00000302420	ENST00000786506.1	n.47+2954T>G		intron_variant	Intron 1 of 1
ENSG00000302420	ENST00000786507.1	n.85-815T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111882 AN: 151864 Hom.: 43404 Cov.: 31

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.736 AC: 111927 AN: 151982 Hom.: 43420 Cov.: 31 AF XY: 0.742 AC XY: 55167 AN XY: 74304

African (AFR) AF: 0.469 AC: 19417 AN: 41392

American (AMR) AF: 0.788 AC: 12020 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2554 AN: 3468

East Asian (EAS) AF: 0.928 AC: 4800 AN: 5170

South Asian (SAS) AF: 0.892 AC: 4300 AN: 4820

European-Finnish (FIN) AF: 0.907 AC: 9597 AN: 10584

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56781 AN: 67986

Other (OTH) AF: 0.732 AC: 1542 AN: 2106

Alfa AF: 0.793 Hom.: 153652

Bravo AF: 0.714

Asia WGS AF: 0.886 AC: 3081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4790694; hg19: chr17-4626354;