rs10982292

Positions:

• chr9-114563011-G-A

Variant summary

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

The XR_930260.2(LOC105376229):​n.200+1357C>T 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 0.0358 in 152,310 control chromosomes in the GnomAD database, including 139 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 0.036 (139 hom., cov: 33)
• Consequence: LOC105376229 XR_930260.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

Genes affected

LOC105376229 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376229	XR_930260.2	n.200+1357C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0357 AC: 5433 AN: 152192 Hom.: 138 Cov.: 33

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0400

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0235

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0358 AC: 5454 AN: 152310 Hom.: 139 Cov.: 33 AF XY: 0.0342 AC XY: 2544 AN XY: 74472

Gnomad4 AFR AF: 0.0542

Gnomad4 AMR AF: 0.0498

Gnomad4 ASJ AF: 0.0400

Gnomad4 EAS AF: 0.0582

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0105

Gnomad4 NFE AF: 0.0235

Gnomad4 OTH AF: 0.0365

Alfa AF: 0.0304 Hom.: 16

Bravo AF: 0.0427

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10982292; hg19: chr9-117325291;