chr2-180076595-C-T

Variant names:

• chr2-180076595-C-T
• rs960224

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.276 AC: 11422 AN: 41420

American (AMR) AF: 0.258 AC: 3940 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1215 AN: 3466

East Asian (EAS) AF: 0.0738 AC: 382 AN: 5176

South Asian (SAS) AF: 0.281 AC: 1355 AN: 4814

European-Finnish (FIN) AF: 0.381 AC: 4010 AN: 10524

Middle Eastern (MID) AF: 0.321 AC: 93 AN: 290

European-Non Finnish (NFE) AF: 0.306 AC: 20780 AN: 67948

Other (OTH) AF: 0.298 AC: 629 AN: 2114

Alfa AF: 0.279 Hom.: 3110

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
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs960224; hg19: chr2-180941322;