9-117950003-G-C

Variant names:

• chr9-117950003-G-C
• rs1252246
• ENST00000665764.1:n.*17-22096G>C

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*17-22096G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,890 control chromosomes in the GnomAD database, including 13,579 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 0.42 (13579 hom., cov: 31)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.5 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.*17-22096G>C		intron_variant	Intron 2 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*16+101848G>C		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1053+101848G>C		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63801 AN: 151772 Hom.: 13565 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.420 AC: 63852 AN: 151890 Hom.: 13579 Cov.: 31 AF XY: 0.417 AC XY: 30963 AN XY: 74220

African (AFR) AF: 0.420 AC: 17386 AN: 41404

American (AMR) AF: 0.510 AC: 7774 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1760 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1797 AN: 5156

South Asian (SAS) AF: 0.316 AC: 1523 AN: 4816

European-Finnish (FIN) AF: 0.323 AC: 3410 AN: 10554

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28783 AN: 67924

Other (OTH) AF: 0.450 AC: 948 AN: 2106

Alfa AF: 0.250 Hom.: 513

Bravo AF: 0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.39
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1252246; hg19: chr9-120712281;