rs757558

Variant names:

• chr17-65565474-G-T
• rs757558
• ENST00000577662.1:n.*61-6738C>A

Variant summary

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

The ENST00000577662.1(ENSG00000266076):​n.*61-6738C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,276 control chromosomes in the GnomAD database, including 1,216 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 0.11 (1216 hom., cov: 33)
• Consequence: ENSG00000266076 ENST00000577662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.824
• Publications: 14 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 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.*61-6738C>A		intron_variant	Intron 3 of 6	2		ENSP00000462418.1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16716 AN: 152158 Hom.: 1217 Cov.: 33

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0825

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.110 AC: 16708 AN: 152276 Hom.: 1216 Cov.: 33 AF XY: 0.108 AC XY: 8030 AN XY: 74444

African (AFR) AF: 0.0307 AC: 1278 AN: 41572

American (AMR) AF: 0.110 AC: 1688 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3468

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5184

South Asian (SAS) AF: 0.157 AC: 759 AN: 4820

European-Finnish (FIN) AF: 0.0825 AC: 875 AN: 10608

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10694 AN: 68008

Other (OTH) AF: 0.135 AC: 285 AN: 2114

Alfa AF: 0.145 Hom.: 1021

Bravo AF: 0.106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.46
DANN	Benign	0.72
PhyloP100		-0.82

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

Other links and lift over

dbSNP: rs757558; hg19: chr17-63561592;