rs12529514

Variant names:

• chr6-14096427-T-C
• rs12529514

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 0.0499 in 152,166 control chromosomes in the GnomAD database, including 351 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 0.050 (351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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: 0.0499 AC: 7586 AN: 152048 Hom.: 352 Cov.: 32

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.0599

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0493

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0499 AC: 7590 AN: 152166 Hom.: 351 Cov.: 32 AF XY: 0.0528 AC XY: 3926 AN XY: 74390

Gnomad4 AFR AF: 0.0159

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.0599

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0748

Gnomad4 NFE AF: 0.0493

Gnomad4 OTH AF: 0.0611

Alfa AF: 0.0515 Hom.: 542

Bravo AF: 0.0445

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12529514; hg19: chr6-14096658;