rs488101

Variant names:

• chr9-117945347-C-T
• rs488101
• ENST00000665764.1:n.*17-26752C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665764.1(ENSG00000285082):​n.*17-26752C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,002 control chromosomes in the GnomAD database, including 37,898 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 0.69 (37898 hom., cov: 31)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 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.*17-26752C>T		intron_variant	Intron 2 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*16+97192C>T		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1053+97192C>T		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105087 AN: 151884 Hom.: 37850 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.692 AC: 105191 AN: 152002 Hom.: 37898 Cov.: 31 AF XY: 0.683 AC XY: 50729 AN XY: 74262

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.706

Alfa AF: 0.673 Hom.: 8135

Bravo AF: 0.718

Asia WGS AF: 0.609 AC: 2118 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs488101; hg19: chr9-120707625; COSMIC: COSV60397318;