9-118033712-T-C

Variant names:

• chr9-118033712-T-C
• rs2416604
• ENST00000665764.1:n.*110-23318T>C

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*110-23318T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,788 control chromosomes in the GnomAD database, including 24,283 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 0.55 (24283 hom., cov: 31)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 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.*110-23318T>C		intron_variant	Intron 3 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*17-23318T>C		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1054-23318T>C		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82742 AN: 151670 Hom.: 24283 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.545 AC: 82765 AN: 151788 Hom.: 24283 Cov.: 31 AF XY: 0.549 AC XY: 40708 AN XY: 74176

African (AFR) AF: 0.318 AC: 13169 AN: 41428

American (AMR) AF: 0.527 AC: 8011 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1859 AN: 3464

East Asian (EAS) AF: 0.605 AC: 3099 AN: 5122

South Asian (SAS) AF: 0.616 AC: 2970 AN: 4818

European-Finnish (FIN) AF: 0.708 AC: 7486 AN: 10570

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44085 AN: 67856

Other (OTH) AF: 0.561 AC: 1184 AN: 2112

Alfa AF: 0.613 Hom.: 121744

Bravo AF: 0.525

Asia WGS AF: 0.570 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.60
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2416604; hg19: chr9-120795990; COSMIC: COSV60397506;