rs12135382

chr1-1163041-C-T

Variant summary

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

The XR_007065348.1(LOC124903818):n.165C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,216 control chromosomes in the GnomAD database, including 18,607 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 0.47 (18607 hom., cov: 36)
• Consequence: LOC124903818 XR_007065348.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

LOC124903818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903818	XR_007065348.1	n.165C>T		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71807 AN: 152098 Hom.: 18601 Cov.: 36

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.472 AC: 71833 AN: 152216 Hom.: 18607 Cov.: 36 AF XY: 0.467 AC XY: 34797 AN XY: 74436

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.498

Alfa AF: 0.517 Hom.: 3269

Bravo AF: 0.475

Asia WGS AF: 0.357 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.5
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12135382; hg19: chr1-1098421;