rs1569159

Variant names:

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

Variant summary

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

Genes affected

ENSG00000225258 (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 (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
ENSG00000304108	ENST00000799803.1	n.219-1961C>A		intron_variant	Intron 3 of 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

African (AFR) AF: 0.0414 AC: 1718 AN: 41510

American (AMR) AF: 0.192 AC: 2927 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3464

East Asian (EAS) AF: 0.202 AC: 1033 AN: 5126

South Asian (SAS) AF: 0.0731 AC: 352 AN: 4818

European-Finnish (FIN) AF: 0.112 AC: 1183 AN: 10590

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0856 AC: 5818 AN: 67954

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.100 Hom.: 159

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
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs1569159; hg19: chr2-181481625;