rs10842388

chr12-24649390-A-G

Variant summary

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

The XR_001749046.2(LOC105369698):n.327-31580T>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 0.482 in 152,026 control chromosomes in the GnomAD database, including 20,736 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 0.48 (20736 hom., cov: 31)
• Consequence: LOC105369698 XR_001749046.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

LOC105369698 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369698	XR_001749046.2	n.327-31580T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73233 AN: 151908 Hom.: 20741 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.482 AC: 73229 AN: 152026 Hom.: 20736 Cov.: 31 AF XY: 0.476 AC XY: 35334 AN XY: 74302

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.456

Alfa AF: 0.544 Hom.: 3912

Bravo AF: 0.446

Asia WGS AF: 0.247 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.57
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10842388; hg19: chr12-24802324;