rs12000794

Variant names:

• chr9-100395233-C-A
• rs12000794
• ENST00000757903.1:n.659-15002C>A

Variant summary

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

The ENST00000757903.1(ENSG00000298775):​n.659-15002C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,154 control chromosomes in the GnomAD database, including 2,030 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 0.16 (2030 hom., cov: 31)
• Consequence: ENSG00000298775 ENST00000757903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624
• Publications: 2 publications found

Genes affected

ENSG00000298775 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 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
ENSG00000298775	ENST00000757903.1	n.659-15002C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24227 AN: 152036 Hom.: 2019 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.160 AC: 24284 AN: 152154 Hom.: 2030 Cov.: 31 AF XY: 0.155 AC XY: 11519 AN XY: 74380

African (AFR) AF: 0.172 AC: 7140 AN: 41506

American (AMR) AF: 0.135 AC: 2061 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3472

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5164

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4822

European-Finnish (FIN) AF: 0.163 AC: 1728 AN: 10588

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12019 AN: 68004

Other (OTH) AF: 0.154 AC: 325 AN: 2110

Alfa AF: 0.168 Hom.: 9724

Bravo AF: 0.158

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs12000794; hg19: chr9-103157515;