chr12-53867372-A-C

Variant names:

• chr12-53867372-A-C
• rs6580967
• ENST00000652339.1:n.509+6494A>C

Variant summary

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

The ENST00000652339.1(ENSG00000286069):​n.509+6494A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 152,122 control chromosomes in the GnomAD database, including 35,606 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 0.68 (35606 hom., cov: 32)
• Consequence: ENSG00000286069 ENST00000652339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 7 publications found

Genes affected

ENSG00000286069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378250	NR_189097.1	n.398+16960A>C		intron_variant	Intron 2 of 2
LOC105378250	NR_189098.1	n.497-7783A>C		intron_variant	Intron 3 of 4
LOC105378250	NR_189099.1	n.591+6494A>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286069	ENST00000652339.1	n.509+6494A>C		intron_variant	Intron 4 of 4
ENSG00000286069	ENST00000654713.2	n.317+16960A>C		intron_variant	Intron 2 of 2
ENSG00000286069	ENST00000656247.1	n.344+16960A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103135 AN: 152004 Hom.: 35597 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.678 AC: 103177 AN: 152122 Hom.: 35606 Cov.: 32 AF XY: 0.673 AC XY: 50028 AN XY: 74354

African (AFR) AF: 0.686 AC: 28464 AN: 41480

American (AMR) AF: 0.544 AC: 8311 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2344 AN: 3462

East Asian (EAS) AF: 0.337 AC: 1746 AN: 5174

South Asian (SAS) AF: 0.734 AC: 3542 AN: 4826

European-Finnish (FIN) AF: 0.703 AC: 7443 AN: 10586

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49220 AN: 67988

Other (OTH) AF: 0.664 AC: 1403 AN: 2112

Alfa AF: 0.700 Hom.: 117796

Bravo AF: 0.661

Asia WGS AF: 0.548 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6580967; hg19: chr12-54261156;