rs4653152

Variant names:

• chr1-33465515-G-A
• rs4653152

Your query was ambiguous. Multiple possible variants found:

• chr1-33465515-G-A
• chr1-33465515-G-C

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 0.258 in 151,902 control chromosomes in the GnomAD database, including 5,226 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 (5226 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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: 0.258 AC: 39187 AN: 151784 Hom.: 5221 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.258 AC: 39208 AN: 151902 Hom.: 5226 Cov.: 31 AF XY: 0.259 AC XY: 19256 AN XY: 74246

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.259

Alfa AF: 0.254 Hom.: 2982

Bravo AF: 0.250

Asia WGS AF: 0.351 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4653152; hg19: chr1-33931116; COSMIC: COSV69405510;