rs1543297

chr12-28066467-A-G

Variant summary

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

The XR_931461.3(LOC105369710):n.156-2580T>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 0.336 in 152,086 control chromosomes in the GnomAD database, including 10,631 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 0.34 (10631 hom., cov: 32)
• Consequence: LOC105369710 XR_931461.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

Genes affected

LOC105369710 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369710	XR_931461.3	n.156-2580T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51000 AN: 151970 Hom.: 10603 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.336 AC: 51078 AN: 152086 Hom.: 10631 Cov.: 32 AF XY: 0.343 AC XY: 25473 AN XY: 74362

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.292

Alfa AF: 0.289 Hom.: 1218

Bravo AF: 0.349

Asia WGS AF: 0.575 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.0
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1543297; hg19: chr12-28219400;