2-80755603-T-C

Position:

• chr2-80755603-T-C

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 0.677 in 151,868 control chromosomes in the GnomAD database, including 35,518 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 0.68 (35518 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80755603T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230975	ENST00000450290.1	n.468+20867A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102740 AN: 151752 Hom.: 35485 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.677 AC: 102824 AN: 151868 Hom.: 35518 Cov.: 32 AF XY: 0.673 AC XY: 49918 AN XY: 74206

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.683

Alfa AF: 0.659 Hom.: 5593

Bravo AF: 0.689

Asia WGS AF: 0.537 AC: 1866 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1946781; hg19: chr2-80982728;