chr9-118564751-C-T

Variant names:

• chr9-118564751-C-T
• rs1335256
• ENST00000770012.1:n.197-17857G>A

Variant summary

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

The ENST00000770012.1(ENSG00000300201):​n.197-17857G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 151,990 control chromosomes in the GnomAD database, including 36,439 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 0.69 (36439 hom., cov: 32)
• Consequence: ENSG00000300201 ENST00000770012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 2 publications found

Genes affected

ENSG00000300201 (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 (NFE) allele frequency at 95% confidence interval = 0.716 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
ENSG00000300201	ENST00000770012.1	n.197-17857G>A		intron_variant	Intron 2 of 5
ENSG00000300201	ENST00000770013.1	n.330-3991G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104708 AN: 151872 Hom.: 36414 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.689 AC: 104784 AN: 151990 Hom.: 36439 Cov.: 32 AF XY: 0.689 AC XY: 51170 AN XY: 74290

African (AFR) AF: 0.636 AC: 26345 AN: 41448

American (AMR) AF: 0.679 AC: 10368 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2871 AN: 3472

East Asian (EAS) AF: 0.560 AC: 2887 AN: 5152

South Asian (SAS) AF: 0.640 AC: 3078 AN: 4812

European-Finnish (FIN) AF: 0.737 AC: 7788 AN: 10572

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49018 AN: 67966

Other (OTH) AF: 0.715 AC: 1505 AN: 2104

Alfa AF: 0.691 Hom.: 6181

Bravo AF: 0.681

Asia WGS AF: 0.598 AC: 2078 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.18
PhyloP100		-0.0030

Splicing

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

Other links and lift over

dbSNP: rs1335256; hg19: chr9-121327029;