rs17287293

chr12-24617944-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001749046.2(LOC105369698):n.327-134T>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 0.121 in 152,256 control chromosomes in the GnomAD database, including 1,333 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 (1333 hom., cov: 33)
• Consequence: LOC105369698 XR_001749046.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

LOC105369698 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369698	XR_001749046.2	n.327-134T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18486 AN: 152138 Hom.: 1331 Cov.: 33

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.121 AC: 18496 AN: 152256 Hom.: 1333 Cov.: 33 AF XY: 0.122 AC XY: 9084 AN XY: 74440

Gnomad4 AFR AF: 0.0457

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.148

Alfa AF: 0.149 Hom.: 3206

Bravo AF: 0.122

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	13
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17287293; hg19: chr12-24770878;