rs1569159

Positions:

• chr2-180616898-C-A

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

Genes affected

(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/exons	MANE	Protein	UniProt
		n.180616898C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225258	ENST00000429816.1	n.226-14427G>T		intron_variant		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;