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. Variant got -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

Genes affected

ENSG00000225087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000225087	ENST00000445976.1	n.229+15966C>T		intron_variant	Intron 2 of 4	3
ENSG00000225087	ENST00000654386.1	n.325+15966C>T		intron_variant	Intron 2 of 3
ENSG00000225087	ENST00000656766.1	n.474+15966C>T		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.483

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1405051; hg19: chr1-73348484;