rs10984756

chr9-119889506-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746919.2(LOC107987122):n.453-14821G>C variant causes a intron, non coding transcript 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: LOC107987122 XR_001746919.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

Genes affected

LOC107987122 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987122	XR_001746919.2	n.453-14821G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0210

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.103

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.15
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10984756; hg19: chr9-122651784; COSMIC: COSV60400282;