rs12724719

Variant names:

• chr1-156693719-G-A
• rs12724719
• ENST00000792154.1:n.203G>A

Variant summary

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

The ENST00000792154.1(ENSG00000285570):​n.203G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,948 control chromosomes in the GnomAD database, including 2,377 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 0.17 (2377 hom., cov: 31)
• Consequence: ENSG00000285570 ENST00000792154.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 5 publications found

Genes affected

ENSG00000285570 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792154.1. 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
	ENSG00000285570	ENST00000792154.1		n.203G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000285570	ENST00000650347.1		n.149+3895G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25853 AN: 151830 Hom.: 2373 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.170 AC: 25881 AN: 151948 Hom.: 2377 Cov.: 31 AF XY: 0.172 AC XY: 12755 AN XY: 74226

African (AFR) AF: 0.190 AC: 7863 AN: 41424

American (AMR) AF: 0.258 AC: 3945 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0671 AC: 233 AN: 3470

East Asian (EAS) AF: 0.149 AC: 768 AN: 5148

South Asian (SAS) AF: 0.155 AC: 747 AN: 4814

European-Finnish (FIN) AF: 0.158 AC: 1668 AN: 10542

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10033 AN: 67972

Other (OTH) AF: 0.169 AC: 355 AN: 2104

Alfa AF: 0.165 Hom.: 1614

Bravo AF: 0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.058
DANN	Benign	0.69
PhyloP100		-2.8

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: rs12724719;

hg19: chr1-156663511;