2-180076595-C-T

Position:

• chr2-180076595-C-T

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 0.29 in 151,928 control chromosomes in the GnomAD database, including 6,661 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 0.29 (6661 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44076 AN: 151810 Hom.: 6650 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.0734

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.290 AC: 44122 AN: 151928 Hom.: 6661 Cov.: 31 AF XY: 0.291 AC XY: 21601 AN XY: 74248

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.0738

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.298

Alfa AF: 0.277 Hom.: 2769

Bravo AF: 0.280

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs960224; hg19: chr2-180941322;