chr2-180649002-G-A

Position:

• chr2-180649002-G-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 0.0901 in 152,058 control chromosomes in the GnomAD database, including 839 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 (839 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.180649002G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000225258	ENST00000429816.1	n.225+43228C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13691 AN: 151940 Hom.: 836 Cov.: 32

Gnomad AFR AF: 0.0414

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0901 AC: 13697 AN: 152058 Hom.: 839 Cov.: 32 AF XY: 0.0939 AC XY: 6976 AN XY: 74312

Gnomad4 AFR AF: 0.0414

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.0727

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0854

Gnomad4 OTH AF: 0.0856

Alfa AF: 0.0907 Hom.: 1618

Bravo AF: 0.0957

Asia WGS AF: 0.116 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs918959; hg19: chr2-181513729;