rs12364283

chr11-113476233-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XR_948024.2(LOC105369501):n.589-380T>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 0.0578 in 150,654 control chromosomes in the GnomAD database, including 322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.058 (322 hom., cov: 32)
• Consequence: LOC105369501 XR_948024.2 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.00500

Genes affected

LOC105369501 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 11-113476233-A-G is Benign according to our data. Variant chr11-113476233-A-G is described in ClinVar as [Benign]. Clinvar id is 1165389.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369501	XR_948024.2	n.589-380T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0579 AC: 8713 AN: 150538 Hom.: 322 Cov.: 32

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.00197

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.0606

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

GnomAD4 genome AF: 0.0578 AC: 8708 AN: 150654 Hom.: 322 Cov.: 32 AF XY: 0.0569 AC XY: 4174 AN XY: 73404

Gnomad4 AFR AF: 0.0239

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0904

Gnomad4 EAS AF: 0.00198

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0693

Gnomad4 NFE AF: 0.0756

Gnomad4 OTH AF: 0.0600

Alfa AF: 0.0723 Hom.: 527

Bravo AF: 0.0537

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Dystonic disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 15, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.1
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12364283; hg19: chr11-113346955;