rs1569159

Variant names:

• chr2-180616898-C-A
• rs1569159
• ENST00000429816.1:n.226-14427G>T

Variant summary

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

The ENST00000429816.1(ENSG00000225258):​n.226-14427G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0902 in 152,016 control chromosomes in the GnomAD database, including 836 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 0.090 (836 hom., cov: 31)
• Consequence: ENSG00000225258 ENST00000429816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

Genes affected

ENSG00000225258 (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 (EAS) allele frequency at 95% confidence interval = 0.191 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
ENSG00000225258	ENST00000429816.1	n.226-14427G>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0903 AC: 13709 AN: 151898 Hom.: 833 Cov.: 31

Gnomad AFR AF: 0.0415

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0856

Gnomad OTH AF: 0.0853

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

GnomAD4 genome AF: 0.0902 AC: 13715 AN: 152016 Hom.: 836 Cov.: 31 AF XY: 0.0938 AC XY: 6973 AN XY: 74308

Gnomad4 AFR AF: 0.0414

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.0731

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0856

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.101 Hom.: 158

Bravo AF: 0.0956

Asia WGS AF: 0.114 AC: 394 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	1.6
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: rs1569159; hg19: chr2-181481625;