12-93930839-A-G

Variant names:

• chr12-93930839-A-G
• rs6538463
• ENST00000550687.1:n.59+12706T>C

Variant summary

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

The ENST00000550687.1(ENSG00000257283):​n.59+12706T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,986 control chromosomes in the GnomAD database, including 13,507 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 0.42 (13507 hom., cov: 32)
• Consequence: ENSG00000257283 ENST00000550687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 4 publications found

Genes affected

ENSG00000257283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369911	NR_135017.1	n.62+12706T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257283	ENST00000550687.1	n.59+12706T>C		intron_variant	Intron 1 of 2	4
ENSG00000257283	ENST00000786429.1	n.197-21834T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63670 AN: 151868 Hom.: 13509 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.419 AC: 63687 AN: 151986 Hom.: 13507 Cov.: 32 AF XY: 0.417 AC XY: 31006 AN XY: 74310

African (AFR) AF: 0.429 AC: 17779 AN: 41436

American (AMR) AF: 0.439 AC: 6695 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2671 AN: 5164

South Asian (SAS) AF: 0.350 AC: 1690 AN: 4826

European-Finnish (FIN) AF: 0.368 AC: 3892 AN: 10562

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27811 AN: 67956

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.412 Hom.: 2217

Bravo AF: 0.429

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.30
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs6538463; hg19: chr12-94324615;