2-53246066-T-C

Variant names:

• chr2-53246066-T-C
• rs195573

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 0.26 in 151,738 control chromosomes in the GnomAD database, including 6,324 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 0.26 (6324 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 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: 0.260 AC: 39446 AN: 151620 Hom.: 6296 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.260 AC: 39511 AN: 151738 Hom.: 6324 Cov.: 31 AF XY: 0.257 AC XY: 19086 AN XY: 74128

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.209

Alfa AF: 0.111 Hom.: 178

Bravo AF: 0.275

Asia WGS AF: 0.141 AC: 490 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs195573; hg19: chr2-53473204;