rs1545843

Variant names:

• chr12-84170289-G-A
• rs1545843
• ENST00000642846.1:n.34+15822G>A

Variant summary

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

The ENST00000642846.1(ENSG00000257729):​n.34+15822G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,840 control chromosomes in the GnomAD database, including 21,256 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 0.52 (21256 hom., cov: 32)
• Consequence: ENSG00000257729 ENST00000642846.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 34 publications found

Genes affected

ENSG00000257729 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984536	XR_001749234.2	n.111+16177C>T		intron_variant	Intron 1 of 3
LOC107984536	XR_001749235.2	n.111+16177C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257729	ENST00000642846.1	n.34+15822G>A		intron_variant	Intron 1 of 7
ENSG00000289309	ENST00000688936.3	n.122+16177C>T		intron_variant	Intron 1 of 2
ENSG00000289309	ENST00000689302.2	n.113+16177C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78759 AN: 151722 Hom.: 21237 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.519 AC: 78818 AN: 151840 Hom.: 21256 Cov.: 32 AF XY: 0.514 AC XY: 38166 AN XY: 74214

African (AFR) AF: 0.660 AC: 27350 AN: 41442

American (AMR) AF: 0.532 AC: 8114 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1835 AN: 5152

South Asian (SAS) AF: 0.593 AC: 2854 AN: 4810

European-Finnish (FIN) AF: 0.361 AC: 3801 AN: 10542

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31202 AN: 67872

Other (OTH) AF: 0.536 AC: 1130 AN: 2108

Alfa AF: 0.479 Hom.: 77394

Bravo AF: 0.539

Asia WGS AF: 0.464 AC: 1608 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.21
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1545843; hg19: chr12-84564068;