rs1251584

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000225605 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635455.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225605	ENST00000635455.1	TSL:5	n.191+24269T>C		intron	N/A
	ENSG00000225605	ENST00000653726.1		n.198-13465T>C		intron	N/A
	ENSG00000225605	ENST00000654326.1		n.246-13465T>C		intron	N/A

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

African (AFR) AF: 0.106 AC: 4380 AN: 41514

American (AMR) AF: 0.249 AC: 3808 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1518 AN: 3468

East Asian (EAS) AF: 0.0299 AC: 155 AN: 5176

South Asian (SAS) AF: 0.213 AC: 1024 AN: 4816

European-Finnish (FIN) AF: 0.318 AC: 3360 AN: 10570

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19386 AN: 67962

Other (OTH) AF: 0.275 AC: 579 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs1251584; hg19: chr1-76424440;