rs12826237

Variant names:

• chr12-75679777-T-C
• rs12826237
• ENST00000552856.1:n.401+12328A>G

Variant summary

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

The ENST00000552856.1(ENSG00000258077):​n.401+12328A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,000 control chromosomes in the GnomAD database, including 737 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 0.094 (737 hom., cov: 31)
• Consequence: ENSG00000258077 ENST00000552856.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 2 publications found

Genes affected

ENSG00000258077 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369844	XR_007063374.1	n.691+12328A>G		intron_variant	Intron 5 of 6
LOC105369844	XR_007063375.1	n.1371+12328A>G		intron_variant	Intron 6 of 15
LOC105369844	XR_007063376.1	n.2298+12328A>G		intron_variant	Intron 4 of 7
LOC105369844	XR_007063377.1	n.2298+12328A>G		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258077	ENST00000552856.1	n.401+12328A>G		intron_variant	Intron 3 of 4	3
ENSG00000286259	ENST00000651075.1	n.322+8881T>C		intron_variant	Intron 4 of 5
ENSG00000258077	ENST00000741371.1	n.527+12328A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14240 AN: 151882 Hom.: 736 Cov.: 31

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0937 AC: 14248 AN: 152000 Hom.: 737 Cov.: 31 AF XY: 0.0938 AC XY: 6965 AN XY: 74272

African (AFR) AF: 0.0371 AC: 1538 AN: 41466

American (AMR) AF: 0.113 AC: 1730 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0975 AC: 338 AN: 3468

East Asian (EAS) AF: 0.0842 AC: 435 AN: 5166

South Asian (SAS) AF: 0.0849 AC: 409 AN: 4818

European-Finnish (FIN) AF: 0.117 AC: 1231 AN: 10566

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8146 AN: 67956

Other (OTH) AF: 0.111 AC: 234 AN: 2108

Alfa AF: 0.114 Hom.: 1241

Bravo AF: 0.0909

Asia WGS AF: 0.0670 AC: 232 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	3.8
DANN	Benign	0.81
PhyloP100		0.42
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12826237; hg19: chr12-76073557;