chr1-25076133-C-T

Variant names:

• chr1-25076133-C-T
• rs10903027
• ENST00000424084.1:n.360+27720G>A

Variant summary

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

The ENST00000424084.1(ENSG00000233755):​n.360+27720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,074 control chromosomes in the GnomAD database, including 6,403 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 0.27 (6403 hom., cov: 32)
• Consequence: ENSG00000233755 ENST00000424084.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772
• Publications: 4 publications found

Genes affected

ENSG00000233755 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424084.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233755	ENST00000424084.1	TSL:3	n.360+27720G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41612 AN: 151956 Hom.: 6398 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.274 AC: 41633 AN: 152074 Hom.: 6403 Cov.: 32 AF XY: 0.285 AC XY: 21192 AN XY: 74336

African (AFR) AF: 0.180 AC: 7465 AN: 41486

American (AMR) AF: 0.413 AC: 6301 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3468

East Asian (EAS) AF: 0.555 AC: 2868 AN: 5170

South Asian (SAS) AF: 0.340 AC: 1640 AN: 4824

European-Finnish (FIN) AF: 0.371 AC: 3919 AN: 10572

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17610 AN: 67966

Other (OTH) AF: 0.264 AC: 557 AN: 2112

Alfa AF: 0.258 Hom.: 2250

Bravo AF: 0.277

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.67
DANN	Benign	0.72
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs10903027; hg19: chr1-25402624;