rs12150466

chr17-44921166-C-T

Variant summary

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

The XR_934781.3(LOC105371793):n.1100+1348C>T 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 0.0511 in 152,242 control chromosomes in the GnomAD database, including 267 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 0.051 (267 hom., cov: 32)
• Consequence: LOC105371793 XR_934781.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

Genes affected

LOC105371793 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371793	XR_934781.3	n.1100+1348C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0512 AC: 7783 AN: 152124 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0251

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.0242

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0511 AC: 7779 AN: 152242 Hom.: 267 Cov.: 32 AF XY: 0.0483 AC XY: 3592 AN XY: 74436

Gnomad4 AFR AF: 0.0250

Gnomad4 AMR AF: 0.0242

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0268

Gnomad4 FIN AF: 0.0505

Gnomad4 NFE AF: 0.0794

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0683 Hom.: 204

Bravo AF: 0.0481

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.2
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12150466; hg19: chr17-42998534;