9-119889620-T-G

Variant names:

• chr9-119889620-T-G
• rs10984758
• ENST00000750211.1:n.102-14935A>C

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.102-14935A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 151,876 control chromosomes in the GnomAD database, including 1,195 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 0.12 (1195 hom., cov: 31)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 2 publications found

Genes affected

ENSG00000297691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750211.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297691	ENST00000750211.1		n.102-14935A>C		intron	N/A
	ENSG00000297691	ENST00000750212.1		n.184-14935A>C		intron	N/A
	ENSG00000297691	ENST00000750213.1		n.121-14935A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17543 AN: 151758 Hom.: 1190 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.0202

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.116 AC: 17564 AN: 151876 Hom.: 1195 Cov.: 31 AF XY: 0.110 AC XY: 8192 AN XY: 74218

African (AFR) AF: 0.185 AC: 7672 AN: 41390

American (AMR) AF: 0.105 AC: 1597 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3468

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5170

South Asian (SAS) AF: 0.0204 AC: 98 AN: 4808

European-Finnish (FIN) AF: 0.0668 AC: 705 AN: 10558

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6970 AN: 67924

Other (OTH) AF: 0.103 AC: 218 AN: 2112

Alfa AF: 0.0691 Hom.: 90

Bravo AF: 0.123

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.4
DANN	Benign	0.80
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs10984758; hg19: chr9-122651898; COSMIC: COSV60400292;