1-25076133-C-T

Position:

• chr1-25076133-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000424084.1(ENSG00000233755):​n.360+27720G>A variant causes a intron, non coding transcript 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: ENST00000424084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000424084.1	n.360+27720G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.264

Alfa AF: 0.276 Hom.: 805

Bravo AF: 0.277

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10903027; hg19: chr1-25402624;