rs12529543

Variant names:

• chr6-76682109-C-T
• rs12529543

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 0.159 in 152,090 control chromosomes in the GnomAD database, including 2,616 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 0.16 (2616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.159 AC: 24209 AN: 151970 Hom.: 2610 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.159 AC: 24236 AN: 152090 Hom.: 2616 Cov.: 32 AF XY: 0.159 AC XY: 11787 AN XY: 74352

African (AFR) AF: 0.294 AC: 12187 AN: 41440

American (AMR) AF: 0.167 AC: 2556 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3472

East Asian (EAS) AF: 0.0949 AC: 491 AN: 5174

South Asian (SAS) AF: 0.102 AC: 491 AN: 4820

European-Finnish (FIN) AF: 0.116 AC: 1228 AN: 10580

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6809 AN: 67992

Other (OTH) AF: 0.138 AC: 291 AN: 2108

Alfa AF: 0.122 Hom.: 4405

Bravo AF: 0.171

Asia WGS AF: 0.111 AC: 390 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	0.31
DANN	Benign	0.25
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs12529543; hg19: chr6-77391826;