rs1017020

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000266076 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577662.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266076	ENST00000577662.1	TSL:2	n.*61-9052T>G		intron	N/A	ENSP00000462418.1	J3KSC3

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

African (AFR) AF: 0.418 AC: 17297 AN: 41368

American (AMR) AF: 0.114 AC: 1732 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3470

East Asian (EAS) AF: 0.132 AC: 684 AN: 5170

South Asian (SAS) AF: 0.172 AC: 828 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1298 AN: 10560

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8174 AN: 67982

Other (OTH) AF: 0.177 AC: 373 AN: 2106

Alfa AF: 0.150 Hom.: 1877

Bravo AF: 0.212

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.51
PhyloP100		0.12

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1017020;

hg19: chr17-63563906;