rs488101

Variant names:

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

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*17-26752C>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
• 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=-0.99).
• 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

African (AFR) AF: 0.899 AC: 37322 AN: 41510

American (AMR) AF: 0.689 AC: 10501 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2523 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3020 AN: 5164

South Asian (SAS) AF: 0.547 AC: 2631 AN: 4810

European-Finnish (FIN) AF: 0.464 AC: 4877 AN: 10518

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42069 AN: 67962

Other (OTH) AF: 0.706 AC: 1494 AN: 2116

Alfa AF: 0.668 Hom.: 13945

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

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