rs10984755

Variant names:

• chr9-119889117-G-A
• rs10984755
• ENST00000750211.1:n.102-14432C>T

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.102-14432C>T 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 152,112 control chromosomes in the GnomAD database, including 1,240 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 (1240 hom., cov: 32)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987122	XR_001746919.2	n.453-14432C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297691	ENST00000750211.1	n.102-14432C>T		intron_variant	Intron 1 of 7
ENSG00000297691	ENST00000750212.1	n.184-14432C>T		intron_variant	Intron 1 of 3
ENSG00000297691	ENST00000750213.1	n.121-14432C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17661 AN: 151994 Hom.: 1235 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.116 AC: 17681 AN: 152112 Hom.: 1240 Cov.: 32 AF XY: 0.111 AC XY: 8265 AN XY: 74346

African (AFR) AF: 0.186 AC: 7729 AN: 41464

American (AMR) AF: 0.106 AC: 1619 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3470

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5184

South Asian (SAS) AF: 0.0212 AC: 102 AN: 4822

European-Finnish (FIN) AF: 0.0671 AC: 711 AN: 10590

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

European-Non Finnish (NFE) AF: 0.103 AC: 6994 AN: 67996

Other (OTH) AF: 0.104 AC: 219 AN: 2110

Alfa AF: 0.111 Hom.: 220

Bravo AF: 0.124

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.59
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10984755; hg19: chr9-122651395; COSMIC: COSV53991058;