2-180490796-G-C

Position:

• chr2-180490796-G-C

Variant summary

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

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 0.26 (3631 hom., cov: 18)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.180490796G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.265 AC: 27978 AN: 105650 Hom.: 3628 Cov.: 18

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.265 AC: 27992 AN: 105690 Hom.: 3631 Cov.: 18 AF XY: 0.274 AC XY: 13424 AN XY: 49006

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.271

Alfa AF: 0.0736 Hom.: 89

Bravo AF: 0.216

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.54
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11692860; hg19: chr2-181355523;