chr2-53246066-T-C

Variant names:

• chr2-53246066-T-C
• rs195573

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 0.26 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.452 AC: 18691 AN: 41334

American (AMR) AF: 0.252 AC: 3843 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3464

East Asian (EAS) AF: 0.121 AC: 621 AN: 5146

South Asian (SAS) AF: 0.104 AC: 501 AN: 4824

European-Finnish (FIN) AF: 0.185 AC: 1944 AN: 10512

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12619 AN: 67908

Other (OTH) AF: 0.209 AC: 441 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs195573; hg19: chr2-53473204;