rs10984756

Variant names:

• chr9-119889506-C-G
• rs10984756
• ENST00000750211.1:n.102-14821G>C

Your query was ambiguous. Multiple possible variants found:

• chr9-119889506-C-G
• chr9-119889506-C-T

Variant summary

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

The ENST00000750211.1(ENSG00000297691):​n.102-14821G>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 152,118 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: 31)
• Consequence: ENSG00000297691 ENST00000750211.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 4 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297691	ENST00000750211.1		n.102-14821G>C		intron	N/A
	ENSG00000297691	ENST00000750212.1		n.184-14821G>C		intron	N/A
	ENSG00000297691	ENST00000750213.1		n.121-14821G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17674 AN: 152000 Hom.: 1235 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0208

Gnomad FIN AF: 0.0672

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: 17695 AN: 152118 Hom.: 1240 Cov.: 31 AF XY: 0.111 AC XY: 8271 AN XY: 74394

African (AFR) AF: 0.187 AC: 7745 AN: 41484

American (AMR) AF: 0.105 AC: 1611 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3472

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5188

South Asian (SAS) AF: 0.0210 AC: 101 AN: 4812

European-Finnish (FIN) AF: 0.0672 AC: 712 AN: 10588

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

European-Non Finnish (NFE) AF: 0.103 AC: 7002 AN: 67978

Other (OTH) AF: 0.103 AC: 218 AN: 2108

Alfa AF: 0.117 Hom.: 136

Bravo AF: 0.124

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.59
PhyloP100		-0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10984756;

hg19: chr9-122651784;

COSMIC: COSV60400282;