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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369710	XR_931461.3	n.156-2580T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

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 v4.3

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;