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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642846.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000257729	ENST00000642846.1		n.34+15822G>A		intron	N/A
	ENSG00000289309	ENST00000688936.3		n.122+16177C>T		intron	N/A
	ENSG00000289309	ENST00000689302.2		n.113+16177C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1545843;

hg19: chr12-84564068;