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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.182 AC: 7563 AN: 41458

American (AMR) AF: 0.355 AC: 5409 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1872 AN: 3462

East Asian (EAS) AF: 0.326 AC: 1668 AN: 5112

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4816

European-Finnish (FIN) AF: 0.477 AC: 5057 AN: 10592

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31007 AN: 67876

Other (OTH) AF: 0.387 AC: 817 AN: 2112

Alfa AF: 0.427 Hom.: 54055

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
PhyloP100		0.23

Splicing

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

Other links and lift over

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