chr9-118580943-A-C

Variant names:

• chr9-118580943-A-C
• rs10125157
• ENST00000770012.1:n.196+12112T>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+12112T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,024 control chromosomes in the GnomAD database, including 806 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 0.087 (806 hom., cov: 32)
• Consequence: ENSG00000300201 ENST00000770012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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+12112T>G		intron_variant	Intron 2 of 5
ENSG00000300201	ENST00000770013.1	n.329+12112T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13230 AN: 151906 Hom.: 808 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0752

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.0871 AC: 13236 AN: 152024 Hom.: 806 Cov.: 32 AF XY: 0.0924 AC XY: 6870 AN XY: 74314

African (AFR) AF: 0.131 AC: 5457 AN: 41502

American (AMR) AF: 0.0748 AC: 1139 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1085 AN: 5148

South Asian (SAS) AF: 0.265 AC: 1277 AN: 4818

European-Finnish (FIN) AF: 0.0677 AC: 718 AN: 10610

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0439 AC: 2981 AN: 67934

Other (OTH) AF: 0.0944 AC: 199 AN: 2108

Alfa AF: 0.0677 Hom.: 197

Bravo AF: 0.0879

Asia WGS AF: 0.218 AC: 756 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	3.6
DANN	Benign	0.66
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs10125157; hg19: chr9-121343221;