rs740026

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000266076 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.340

Alfa AF: 0.421 Hom.: 7679

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

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: rs740026; hg19: chr17-63561681;