chr12-115132241-G-A

Variant names:

• chr12-115132241-G-A
• rs35426
• ENST00000812050.1:n.251-2216G>A

Variant summary

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

The ENST00000812050.1(ENSG00000305627):​n.251-2216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,090 control chromosomes in the GnomAD database, including 38,174 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 0.69 (38174 hom., cov: 32)
• Consequence: ENSG00000305627 ENST00000812050.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 5 publications found

Genes affected

ENSG00000305627 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 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
ENSG00000305627	ENST00000812050.1	n.251-2216G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105083 AN: 151972 Hom.: 38101 Cov.: 32

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.692 AC: 105213 AN: 152090 Hom.: 38174 Cov.: 32 AF XY: 0.689 AC XY: 51213 AN XY: 74328

African (AFR) AF: 0.925 AC: 38442 AN: 41560

American (AMR) AF: 0.630 AC: 9629 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2312 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4088 AN: 5160

South Asian (SAS) AF: 0.637 AC: 3054 AN: 4798

European-Finnish (FIN) AF: 0.569 AC: 6005 AN: 10562

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39676 AN: 67946

Other (OTH) AF: 0.675 AC: 1428 AN: 2114

Alfa AF: 0.615 Hom.: 63641

Bravo AF: 0.704

Asia WGS AF: 0.734 AC: 2549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.67
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs35426; hg19: chr12-115570046;