9-117915442-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000285082	ENST00000665764.1	n.*17-56657G>T		intron_variant	Intron 2 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*16+67287G>T		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1053+67287G>T		intron_variant	Intron 7 of 12

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

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.631

Alfa AF: 0.598 Hom.: 5864

Bravo AF: 0.617

Asia WGS AF: 0.531 AC: 1846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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