9-117995092-C-T

Variant names:

• chr9-117995092-C-T
• rs2245960
• ENST00000665764.1:n.*109+22901C>T

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*109+22901C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,022 control chromosomes in the GnomAD database, including 2,754 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 0.19 (2754 hom., cov: 32)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 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.*109+22901C>T		intron_variant	Intron 3 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*17-61938C>T		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1054-61938C>T		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28134 AN: 151904 Hom.: 2748 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.185 AC: 28154 AN: 152022 Hom.: 2754 Cov.: 32 AF XY: 0.184 AC XY: 13690 AN XY: 74284

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.199

Alfa AF: 0.199 Hom.: 6332

Bravo AF: 0.181

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2245960; hg19: chr9-120757370;