ENST00000665764.1:n.*17-9290A>C

Variant names:

• chr9-117962809-A-C
• rs2151370
• ENST00000665764.1:n.*17-9290A>C

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*17-9290A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,106 control chromosomes in the GnomAD database, including 9,306 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 0.34 (9306 hom., cov: 33)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630

Genes affected

ENSG00000285082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 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.*17-9290A>C		intron_variant	Intron 2 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*17-94221A>C		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1054-94221A>C		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51085 AN: 151988 Hom.: 9301 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.336 AC: 51107 AN: 152106 Hom.: 9306 Cov.: 33 AF XY: 0.344 AC XY: 25576 AN XY: 74348

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.313

Alfa AF: 0.355 Hom.: 1663

Bravo AF: 0.315

Asia WGS AF: 0.394 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2151370; hg19: chr9-120725087;