9-118584139-T-C

Variant names:

• chr9-118584139-T-C
• rs1572299
• ENST00000770012.1:n.196+8916A>G

Variant summary

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

The ENST00000770012.1(ENSG00000300201):​n.196+8916A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,816 control chromosomes in the GnomAD database, including 12,078 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 0.35 (12078 hom., cov: 31)
• Consequence: ENSG00000300201 ENST00000770012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 16 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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.196+8916A>G		intron_variant	Intron 2 of 5
ENSG00000300201	ENST00000770013.1	n.329+8916A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53161 AN: 151704 Hom.: 12083 Cov.: 31

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.0124

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.350 AC: 53140 AN: 151816 Hom.: 12078 Cov.: 31 AF XY: 0.345 AC XY: 25587 AN XY: 74206

African (AFR) AF: 0.0996 AC: 4122 AN: 41388

American (AMR) AF: 0.335 AC: 5099 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2171 AN: 3464

East Asian (EAS) AF: 0.0126 AC: 65 AN: 5144

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4812

European-Finnish (FIN) AF: 0.500 AC: 5265 AN: 10524

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33902 AN: 67944

Other (OTH) AF: 0.391 AC: 822 AN: 2102

Alfa AF: 0.434 Hom.: 39759

Bravo AF: 0.328

Asia WGS AF: 0.131 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.51
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1572299; hg19: chr9-121346417;