rs740026

Variant names:

• chr17-65565563-G-A
• rs740026
• ENST00000577662.1:n.*61-6827C>T

Variant summary

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

The ENST00000577662.1(ENSG00000266076):​n.*61-6827C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,120 control chromosomes in the GnomAD database, including 11,122 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 0.35 (11122 hom., cov: 33)
• Consequence: ENSG00000266076 ENST00000577662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 15 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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.*61-6827C>T		intron_variant	Intron 3 of 6	2		ENSP00000462418.1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53725 AN: 152002 Hom.: 11121 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.353 AC: 53729 AN: 152120 Hom.: 11122 Cov.: 33 AF XY: 0.354 AC XY: 26325 AN XY: 74352

African (AFR) AF: 0.129 AC: 5362 AN: 41504

American (AMR) AF: 0.425 AC: 6489 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1645 AN: 5174

South Asian (SAS) AF: 0.431 AC: 2076 AN: 4822

European-Finnish (FIN) AF: 0.446 AC: 4710 AN: 10572

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30807 AN: 67978

Other (OTH) AF: 0.340 AC: 718 AN: 2112

Alfa AF: 0.416 Hom.: 12413

Bravo AF: 0.345

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.3
DANN	Benign	0.78
PhyloP100		-0.55

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: rs740026; hg19: chr17-63561681;