9-117750161-C-T

Variant names:

• chr9-117750161-C-T
• rs756135
• ENST00000697666.1:c.140+41432C>T

Variant summary

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

The ENST00000697666.1(ENSG00000285082):​c.140+41432C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 152,004 control chromosomes in the GnomAD database, including 15,648 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 0.44 (15648 hom., cov: 32)
• Consequence: ENSG00000285082 ENST00000697666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 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	ENST00000697666.1	c.140+41432C>T		intron_variant	Intron 3 of 4			ENSP00000513391.1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67095 AN: 151886 Hom.: 15644 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.442 AC: 67137 AN: 152004 Hom.: 15648 Cov.: 32 AF XY: 0.443 AC XY: 32950 AN XY: 74310

African (AFR) AF: 0.345 AC: 14290 AN: 41452

American (AMR) AF: 0.429 AC: 6558 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1719 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4512 AN: 5162

South Asian (SAS) AF: 0.569 AC: 2743 AN: 4818

European-Finnish (FIN) AF: 0.431 AC: 4552 AN: 10556

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.460 AC: 31236 AN: 67960

Other (OTH) AF: 0.455 AC: 961 AN: 2110

Alfa AF: 0.368 Hom.: 1609

Bravo AF: 0.439

Asia WGS AF: 0.680 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.25
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs756135; hg19: chr9-120512439;