ENST00000799978.1:n.142+4516A>G

Variant names:

• chr17-55568879-T-C
• rs17819558
• ENST00000799978.1:n.142+4516A>G

Variant summary

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

The ENST00000799978.1(ENSG00000304133):​n.142+4516A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,114 control chromosomes in the GnomAD database, including 2,629 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 0.18 (2629 hom., cov: 32)
• Consequence: ENSG00000304133 ENST00000799978.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 1 publications found

Genes affected

ENSG00000304133 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 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
ENSG00000304133	ENST00000799978.1	n.142+4516A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26622 AN: 151996 Hom.: 2625 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.175 AC: 26626 AN: 152114 Hom.: 2629 Cov.: 32 AF XY: 0.172 AC XY: 12824 AN XY: 74348

African (AFR) AF: 0.110 AC: 4578 AN: 41528

American (AMR) AF: 0.122 AC: 1862 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1234 AN: 5168

South Asian (SAS) AF: 0.148 AC: 715 AN: 4816

European-Finnish (FIN) AF: 0.204 AC: 2161 AN: 10578

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14657 AN: 67960

Other (OTH) AF: 0.189 AC: 399 AN: 2110

Alfa AF: 0.197 Hom.: 2072

Bravo AF: 0.166

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.75
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs17819558; hg19: chr17-53646240;