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

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

Gnomad4 AFR AF: 0.0307 AC: 0.0307418 AN: 0.0307418

Gnomad4 AMR AF: 0.110 AC: 0.110327 AN: 0.110327

Gnomad4 ASJ AF: 0.243 AC: 0.242791 AN: 0.242791

Gnomad4 EAS AF: 0.0106 AC: 0.0106096 AN: 0.0106096

Gnomad4 SAS AF: 0.157 AC: 0.157469 AN: 0.157469

Gnomad4 FIN AF: 0.0825 AC: 0.0824849 AN: 0.0824849

Gnomad4 NFE AF: 0.157 AC: 0.157246 AN: 0.157246

Gnomad4 OTH AF: 0.135 AC: 0.134816 AN: 0.134816

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

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: rs757558; hg19: chr17-63561592;