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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903876	XR_007065537.1	n.282+8349T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307540	ENST00000826972.1	n.204-12303T>G		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs1555025; hg19: chr1-23886935; COSMIC: COSV65800882;