rs12518194

Variant names:

• chr5-25951452-A-G
• rs12518194

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 0.275 in 151,748 control chromosomes in the GnomAD database, including 7,310 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 0.28 (7310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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: 0.275 AC: 41761 AN: 151630 Hom.: 7309 Cov.: 32

Gnomad AFR AF: 0.0698

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.275 AC: 41767 AN: 151748 Hom.: 7310 Cov.: 32 AF XY: 0.278 AC XY: 20575 AN XY: 74138

Gnomad4 AFR AF: 0.0697

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.301

Alfa AF: 0.338 Hom.: 4642

Bravo AF: 0.256

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12518194; hg19: chr5-25951561; COSMIC: COSV54957365;