rs1543297

Variant names:

• chr12-28066467-A-G
• rs1543297
• XR_931461.3:n.156-2580T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931461.3(LOC105369710):​n.156-2580T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 7 publications found

Genes affected

LOC105369710 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.548 AC: 22746 AN: 41472

American (AMR) AF: 0.321 AC: 4904 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3468

East Asian (EAS) AF: 0.650 AC: 3345 AN: 5144

South Asian (SAS) AF: 0.399 AC: 1923 AN: 4818

European-Finnish (FIN) AF: 0.274 AC: 2897 AN: 10590

Middle Eastern (MID) AF: 0.297 AC: 86 AN: 290

European-Non Finnish (NFE) AF: 0.201 AC: 13651 AN: 67996

Other (OTH) AF: 0.292 AC: 616 AN: 2110

Alfa AF: 0.297 Hom.: 1328

Bravo AF: 0.349

Asia WGS AF: 0.575 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.64
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1543297; hg19: chr12-28219400;