rs12153325

Variant names:

• chr5-52565441-T-C
• rs12153325

Your query was ambiguous. Multiple possible variants found:

• chr5-52565441-T-C
• chr5-52565441-T-G

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 0.365 in 151,852 control chromosomes in the GnomAD database, including 11,330 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 0.37 (11330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 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: 0.366 AC: 55464 AN: 151734 Hom.: 11330 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.365 AC: 55480 AN: 151852 Hom.: 11330 Cov.: 32 AF XY: 0.364 AC XY: 27019 AN XY: 74192

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.387

Alfa AF: 0.440 Hom.: 24970

Bravo AF: 0.352

Asia WGS AF: 0.300 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12153325; hg19: chr5-51861275; COSMIC: COSV60129811;