rs1017020

Variant names:

• chr17-65567788-A-C
• rs1017020
• ENST00000577662.1:n.*61-9052T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577662.1(ENSG00000266076):​n.*61-9052T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 151,932 control chromosomes in the GnomAD database, including 4,574 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 0.20 (4574 hom., cov: 31)
• Consequence: ENSG00000266076 ENST00000577662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

ENSG00000266076 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 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
ENSG00000266076	ENST00000577662.1	n.*61-9052T>G		intron_variant	Intron 3 of 6	2		ENSP00000462418.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30944 AN: 151812 Hom.: 4552 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.204 AC: 31008 AN: 151932 Hom.: 4574 Cov.: 31 AF XY: 0.201 AC XY: 14941 AN XY: 74288

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.177

Alfa AF: 0.146 Hom.: 1291

Bravo AF: 0.212

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1017020; hg19: chr17-63563906;