12-90203038-T-C

Variant names:

• chr12-90203038-T-C
• rs1438993
• ENST00000723053.1:n.125-25324A>G

Variant summary

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

The ENST00000723053.1(ENSG00000294351):​n.125-25324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,974 control chromosomes in the GnomAD database, including 39,681 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 0.72 (39681 hom., cov: 31)
• Consequence: ENSG00000294351 ENST00000723053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 3 publications found

Genes affected

ENSG00000294351 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 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
ENSG00000294351	ENST00000723053.1	n.125-25324A>G		intron_variant	Intron 1 of 1
ENSG00000294351	ENST00000723054.1	n.286+21748A>G		intron_variant	Intron 3 of 3
ENSG00000294351	ENST00000723055.1	n.139+21748A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109442 AN: 151856 Hom.: 39642 Cov.: 31

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.721 AC: 109546 AN: 151974 Hom.: 39681 Cov.: 31 AF XY: 0.716 AC XY: 53150 AN XY: 74226

African (AFR) AF: 0.765 AC: 31740 AN: 41492

American (AMR) AF: 0.669 AC: 10202 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2310 AN: 3472

East Asian (EAS) AF: 0.578 AC: 2965 AN: 5134

South Asian (SAS) AF: 0.694 AC: 3350 AN: 4828

European-Finnish (FIN) AF: 0.660 AC: 6957 AN: 10542

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49563 AN: 67932

Other (OTH) AF: 0.728 AC: 1540 AN: 2116

Alfa AF: 0.722 Hom.: 121218

Bravo AF: 0.722

Asia WGS AF: 0.636 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.47
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1438993; hg19: chr12-90596815;