9-118576812-A-G

Variant names:

• chr9-118576812-A-G
• rs10984096
• ENST00000770012.1:n.196+16243T>C

Variant summary

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

The ENST00000770012.1(ENSG00000300201):​n.196+16243T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,558 control chromosomes in the GnomAD database, including 3,256 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 0.20 (3256 hom., cov: 32)
• Consequence: ENSG00000300201 ENST00000770012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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+16243T>C		intron_variant	Intron 2 of 5
ENSG00000300201	ENST00000770013.1	n.330-16052T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30646 AN: 151440 Hom.: 3252 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.202 AC: 30682 AN: 151558 Hom.: 3256 Cov.: 32 AF XY: 0.202 AC XY: 14936 AN XY: 74084

African (AFR) AF: 0.255 AC: 10564 AN: 41398

American (AMR) AF: 0.249 AC: 3786 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 383 AN: 3454

East Asian (EAS) AF: 0.189 AC: 973 AN: 5150

South Asian (SAS) AF: 0.0941 AC: 454 AN: 4826

European-Finnish (FIN) AF: 0.175 AC: 1845 AN: 10554

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12010 AN: 67684

Other (OTH) AF: 0.190 AC: 401 AN: 2108

Alfa AF: 0.174 Hom.: 1426

Bravo AF: 0.212

Asia WGS AF: 0.143 AC: 494 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10984096; hg19: chr9-121339090;