rs12529093

Variant names:

• chr6-32448081-A-G
• rs12529093
• ENST00000766007.1:n.163-9821T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000766007.1(ENSG00000299747):​n.163-9821T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,204 control chromosomes in the GnomAD database, including 1,422 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 0.13 (1422 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 13 publications found

Genes affected

ENSG00000299747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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
ENSG00000299747	ENST00000766007.1	n.163-9821T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19309 AN: 152086 Hom.: 1422 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.127 AC: 19327 AN: 152204 Hom.: 1422 Cov.: 32 AF XY: 0.130 AC XY: 9696 AN XY: 74388

African (AFR) AF: 0.0848 AC: 3524 AN: 41562

American (AMR) AF: 0.107 AC: 1639 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3470

East Asian (EAS) AF: 0.0424 AC: 220 AN: 5190

South Asian (SAS) AF: 0.141 AC: 681 AN: 4828

European-Finnish (FIN) AF: 0.220 AC: 2321 AN: 10574

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10093 AN: 67984

Other (OTH) AF: 0.124 AC: 261 AN: 2110

Alfa AF: 0.132 Hom.: 2273

Bravo AF: 0.116

Asia WGS AF: 0.0980 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.45
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs12529093; hg19: chr6-32415858;