ENST00000590144.1:n.116-1004A>C

Variant names:

• chr17-35189896-A-C
• rs4796049
• ENST00000590144.1:n.116-1004A>C

Variant summary

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

The ENST00000590144.1(ENSG00000266981):​n.116-1004A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 151,762 control chromosomes in the GnomAD database, including 813 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 0.093 (813 hom., cov: 32)
• Consequence: ENSG00000266981 ENST00000590144.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 1 publications found

Genes affected

ENSG00000266981 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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
ENSG00000266981	ENST00000590144.1	n.116-1004A>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14007 AN: 151642 Hom.: 809 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0925

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

GnomAD4 genome AF: 0.0925 AC: 14041 AN: 151762 Hom.: 813 Cov.: 32 AF XY: 0.0981 AC XY: 7281 AN XY: 74200

African (AFR) AF: 0.104 AC: 4308 AN: 41260

American (AMR) AF: 0.173 AC: 2637 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0404 AC: 140 AN: 3466

East Asian (EAS) AF: 0.209 AC: 1078 AN: 5164

South Asian (SAS) AF: 0.109 AC: 523 AN: 4800

European-Finnish (FIN) AF: 0.114 AC: 1207 AN: 10556

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0565 AC: 3842 AN: 67962

Other (OTH) AF: 0.0929 AC: 195 AN: 2098

Alfa AF: 0.0839 Hom.: 88

Bravo AF: 0.0968

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.8
DANN	Benign	0.22
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4796049; hg19: chr17-33516915;