rs1251584

Variant names:

• chr1-75958755-T-C
• rs1251584
• ENST00000635455.1:n.191+24269T>C

Variant summary

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

The ENST00000635455.1(ENSG00000225605):​n.191+24269T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,100 control chromosomes in the GnomAD database, including 4,552 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 0.23 (4552 hom., cov: 31)
• Consequence: ENSG00000225605 ENST00000635455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

Genes affected

ENSG00000225605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225605	ENST00000635455.1	n.191+24269T>C		intron_variant	Intron 2 of 7	5
ENSG00000225605	ENST00000653726.1	n.198-13465T>C		intron_variant	Intron 2 of 7
ENSG00000225605	ENST00000654326.1	n.246-13465T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34400 AN: 151982 Hom.: 4549 Cov.: 31

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.226 AC: 34403 AN: 152100 Hom.: 4552 Cov.: 31 AF XY: 0.227 AC XY: 16859 AN XY: 74354

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.0299

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.275

Alfa AF: 0.256 Hom.: 937

Bravo AF: 0.219

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1251584; hg19: chr1-76424440;