ENST00000665764.1:n.*17-56657G>T

Variant names:

• chr9-117915442-G-T
• rs4837527
• ENST00000665764.1:n.*17-56657G>T

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*17-56657G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,524 control chromosomes in the GnomAD database, including 27,606 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 0.60 (27606 hom., cov: 31)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 3 publications found

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665764.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285082	ENST00000665764.1		n.*17-56657G>T		intron	N/A	ENSP00000499745.1
	ENSG00000285082	ENST00000697636.1		n.*16+67287G>T		intron	N/A	ENSP00000513366.1
	ENSG00000284977	ENST00000697639.1		n.1053+67287G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90894 AN: 151406 Hom.: 27581 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.600 AC: 90961 AN: 151524 Hom.: 27606 Cov.: 31 AF XY: 0.595 AC XY: 44055 AN XY: 74020

African (AFR) AF: 0.659 AC: 27268 AN: 41366

American (AMR) AF: 0.640 AC: 9728 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2166 AN: 3464

East Asian (EAS) AF: 0.530 AC: 2724 AN: 5142

South Asian (SAS) AF: 0.508 AC: 2446 AN: 4814

European-Finnish (FIN) AF: 0.446 AC: 4700 AN: 10532

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 39882 AN: 67712

Other (OTH) AF: 0.631 AC: 1323 AN: 2098

Alfa AF: 0.602 Hom.: 9937

Bravo AF: 0.617

Asia WGS AF: 0.531 AC: 1846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.26
PhyloP100		0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4837527; hg19: chr9-120677720; COSMIC: COSV60397122;