rs12529514

Variant names:

• chr6-14096427-T-C
• rs12529514

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 0.0499 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
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0159 AC: 660 AN: 41520

American (AMR) AF: 0.0420 AC: 643 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0599 AC: 208 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1068 AN: 5156

South Asian (SAS) AF: 0.141 AC: 678 AN: 4816

European-Finnish (FIN) AF: 0.0748 AC: 792 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0493 AC: 3349 AN: 67990

Other (OTH) AF: 0.0611 AC: 129 AN: 2112

Alfa AF: 0.0501 Hom.: 1209

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12529514; hg19: chr6-14096658;