1-23560444-T-G

Variant names:

• chr1-23560444-T-G
• rs1555025
• ENST00000826972.1:n.204-12303T>G

Variant summary

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

The ENST00000826972.1(ENSG00000307540):​n.204-12303T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 150,996 control chromosomes in the GnomAD database, including 23,883 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 0.56 (23883 hom., cov: 28)
• Consequence: ENSG00000307540 ENST00000826972.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 3 publications found

Genes affected

ENSG00000307540 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826972.1. 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
	ENSG00000307540	ENST00000826972.1		n.204-12303T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84269 AN: 150880 Hom.: 23851 Cov.: 28

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.559 AC: 84358 AN: 150996 Hom.: 23883 Cov.: 28 AF XY: 0.556 AC XY: 41010 AN XY: 73700

African (AFR) AF: 0.601 AC: 24647 AN: 40982

American (AMR) AF: 0.543 AC: 8227 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2025 AN: 3462

East Asian (EAS) AF: 0.836 AC: 4311 AN: 5158

South Asian (SAS) AF: 0.404 AC: 1935 AN: 4794

European-Finnish (FIN) AF: 0.505 AC: 5233 AN: 10360

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36162 AN: 67818

Other (OTH) AF: 0.561 AC: 1165 AN: 2078

Alfa AF: 0.546 Hom.: 61778

Bravo AF: 0.564

Asia WGS AF: 0.559 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		0.32

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: rs1555025;

hg19: chr1-23886935;

COSMIC: COSV65800882;