9-117966399-G-T

Variant names:

• chr9-117966399-G-T
• rs2780244
• ENST00000665764.1:n.*17-5700G>T

Variant summary

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

The ENST00000665764.1(ENSG00000285082):​n.*17-5700G>T 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 151,840 control chromosomes in the GnomAD database, including 9,312 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 (9312 hom., cov: 32)
• Consequence: ENSG00000285082 ENST00000665764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 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.*17-5700G>T		intron_variant	Intron 2 of 6			ENSP00000499745.1
ENSG00000285082	ENST00000697636.1	n.*17-90631G>T		intron_variant	Intron 2 of 5			ENSP00000513366.1
ENSG00000284977	ENST00000697639.1	n.1054-90631G>T		intron_variant	Intron 7 of 12

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51027 AN: 151722 Hom.: 9308 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.336 AC: 51048 AN: 151840 Hom.: 9312 Cov.: 32 AF XY: 0.344 AC XY: 25536 AN XY: 74186

African (AFR) AF: 0.198 AC: 8200 AN: 41398

American (AMR) AF: 0.328 AC: 5000 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2117 AN: 5132

South Asian (SAS) AF: 0.458 AC: 2199 AN: 4806

European-Finnish (FIN) AF: 0.539 AC: 5673 AN: 10518

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25820 AN: 67950

Other (OTH) AF: 0.312 AC: 656 AN: 2100

Alfa AF: 0.272 Hom.: 1058

Bravo AF: 0.315

Asia WGS AF: 0.393 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.59
DANN	Benign	0.64
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2780244; hg19: chr9-120728677;