XR_948024.2:n.589-380T>C

Variant names:

• chr11-113476233-A-G
• rs12364283
• XR_948024.2:n.589-380T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The XR_948024.2(LOC105369501):​n.589-380T>C variant causes a intron 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.00500
• Publications: 78 publications found

Genes affected

LOC105369501 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
LOC105369501	XR_948024.2	n.589-380T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0239 AC: 980 AN: 40932

American (AMR) AF: 0.0492 AC: 743 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.0904 AC: 313 AN: 3462

East Asian (EAS) AF: 0.00198 AC: 10 AN: 5058

South Asian (SAS) AF: 0.102 AC: 486 AN: 4776

European-Finnish (FIN) AF: 0.0693 AC: 711 AN: 10260

Middle Eastern (MID) AF: 0.107 AC: 31 AN: 290

European-Non Finnish (NFE) AF: 0.0756 AC: 5125 AN: 67768

Other (OTH) AF: 0.0600 AC: 125 AN: 2084

Alfa AF: 0.0675 Hom.: 1152

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

Jan 14, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.66
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs12364283; hg19: chr11-113346955;