chr12-126531637-A-G

Variant names:

• chr12-126531637-A-G
• rs2215396
• ENST00000773832.1:n.833-2325T>C

Variant summary

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

The ENST00000773832.1(ENSG00000300751):​n.833-2325T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,036 control chromosomes in the GnomAD database, including 37,011 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 0.67 (37011 hom., cov: 32)
• Consequence: ENSG00000300751 ENST00000773832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 2 publications found

Genes affected

ENSG00000300751 (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 (EAS) allele frequency at 95% confidence interval = 0.934 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
ENSG00000300751	ENST00000773832.1	n.833-2325T>C		intron_variant	Intron 3 of 3
ENSG00000300751	ENST00000773833.1	n.835-2325T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101981 AN: 151918 Hom.: 36995 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.671 AC: 102038 AN: 152036 Hom.: 37011 Cov.: 32 AF XY: 0.679 AC XY: 50458 AN XY: 74322

African (AFR) AF: 0.372 AC: 15431 AN: 41434

American (AMR) AF: 0.772 AC: 11797 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2153 AN: 3470

East Asian (EAS) AF: 0.956 AC: 4921 AN: 5148

South Asian (SAS) AF: 0.815 AC: 3925 AN: 4814

European-Finnish (FIN) AF: 0.836 AC: 8858 AN: 10594

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.774 AC: 52643 AN: 67984

Other (OTH) AF: 0.677 AC: 1430 AN: 2112

Alfa AF: 0.734 Hom.: 51623

Bravo AF: 0.655

Asia WGS AF: 0.854 AC: 2965 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2215396; hg19: chr12-127016183;