2-194007459-C-G

Variant names:

• chr2-194007459-C-G
• rs2176528

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 0.266 in 151,974 control chromosomes in the GnomAD database, including 6,312 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 0.27 (6312 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.266 AC: 40358 AN: 151856 Hom.: 6303 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.266 AC: 40373 AN: 151974 Hom.: 6312 Cov.: 32 AF XY: 0.272 AC XY: 20179 AN XY: 74282

African (AFR) AF: 0.133 AC: 5500 AN: 41466

American (AMR) AF: 0.409 AC: 6251 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3466

East Asian (EAS) AF: 0.623 AC: 3212 AN: 5152

South Asian (SAS) AF: 0.387 AC: 1866 AN: 4818

European-Finnish (FIN) AF: 0.209 AC: 2209 AN: 10558

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.285 AC: 19341 AN: 67942

Other (OTH) AF: 0.298 AC: 627 AN: 2104

Alfa AF: 0.275 Hom.: 3496

Bravo AF: 0.276

Asia WGS AF: 0.467 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.57
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2176528; hg19: chr2-194872183;