ENST00000720595.1:n.176-11454A>C

Variant names:

• chr4-119322874-A-C
• rs10034579
• ENST00000720595.1:n.176-11454A>C

Variant summary

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

The ENST00000720595.1(ENSG00000294020):​n.176-11454A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,982 control chromosomes in the GnomAD database, including 24,451 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 0.57 (24451 hom., cov: 32)
• Consequence: ENSG00000294020 ENST00000720595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 5 publications found

Genes affected

ENSG00000294020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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
ENSG00000294020	ENST00000720595.1	n.176-11454A>C		intron_variant	Intron 1 of 5
ENSG00000294020	ENST00000720596.1	n.224-11454A>C		intron_variant	Intron 1 of 6
ENSG00000294020	ENST00000720597.1	n.238-11454A>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86072 AN: 151864 Hom.: 24418 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.567 AC: 86171 AN: 151982 Hom.: 24451 Cov.: 32 AF XY: 0.564 AC XY: 41918 AN XY: 74314

African (AFR) AF: 0.559 AC: 23166 AN: 41434

American (AMR) AF: 0.605 AC: 9240 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2154 AN: 3466

East Asian (EAS) AF: 0.628 AC: 3244 AN: 5168

South Asian (SAS) AF: 0.533 AC: 2568 AN: 4822

European-Finnish (FIN) AF: 0.511 AC: 5406 AN: 10572

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38548 AN: 67928

Other (OTH) AF: 0.599 AC: 1265 AN: 2112

Alfa AF: 0.529 Hom.: 4399

Bravo AF: 0.579

Asia WGS AF: 0.635 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.52
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10034579; hg19: chr4-120244029;