rs1405051

Variant names:

• chr1-72882801-G-A
• rs1405051
• ENST00000445976.1:n.229+15966C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-72882801-G-A
• chr1-72882801-G-C
• chr1-72882801-G-T

Variant summary

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

The ENST00000445976.1(ENSG00000225087):​n.229+15966C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,844 control chromosomes in the GnomAD database, including 16,787 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 0.47 (16787 hom., cov: 32)
• Consequence: ENSG00000225087 ENST00000445976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 4 publications found

Genes affected

ENSG00000225087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445976.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225087	ENST00000445976.1	TSL:3	n.229+15966C>T		intron	N/A
	ENSG00000225087	ENST00000654386.1		n.325+15966C>T		intron	N/A
	ENSG00000225087	ENST00000656766.1		n.474+15966C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70696 AN: 151728 Hom.: 16788 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.466 AC: 70729 AN: 151844 Hom.: 16787 Cov.: 32 AF XY: 0.469 AC XY: 34797 AN XY: 74198

African (AFR) AF: 0.451 AC: 18687 AN: 41440

American (AMR) AF: 0.411 AC: 6269 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3707 AN: 5146

South Asian (SAS) AF: 0.572 AC: 2759 AN: 4826

European-Finnish (FIN) AF: 0.440 AC: 4635 AN: 10534

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31329 AN: 67856

Other (OTH) AF: 0.483 AC: 1021 AN: 2114

Alfa AF: 0.332 Hom.: 883

Bravo AF: 0.460

Asia WGS AF: 0.621 AC: 2158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.040
DANN	Benign	0.22
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1405051; hg19: chr1-73348484;