12-130012927-A-G

Variant names:

• chr12-130012927-A-G
• rs1624802
• ENST00000793812.1:n.335+2603A>G

Variant summary

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

The ENST00000793812.1(ENSG00000256298):​n.335+2603A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,762 control chromosomes in the GnomAD database, including 15,273 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 0.44 (15273 hom., cov: 31)
• Consequence: ENSG00000256298 ENST00000793812.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 4 publications found

Genes affected

ENSG00000256298 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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
ENSG00000256298	ENST00000793812.1	n.335+2603A>G		intron_variant	Intron 1 of 1
ENSG00000256298	ENST00000793813.1	n.633+2603A>G		intron_variant	Intron 1 of 1
ENSG00000256298	ENST00000793815.1	n.300-16817A>G		intron_variant	Intron 2 of 2
ENSG00000256298	ENST00000793816.1	n.337+13030A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66138 AN: 151648 Hom.: 15260 Cov.: 31

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.436 AC: 66200 AN: 151762 Hom.: 15273 Cov.: 31 AF XY: 0.444 AC XY: 32945 AN XY: 74158

African (AFR) AF: 0.405 AC: 16722 AN: 41332

American (AMR) AF: 0.531 AC: 8086 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1844 AN: 3466

East Asian (EAS) AF: 0.843 AC: 4338 AN: 5148

South Asian (SAS) AF: 0.583 AC: 2804 AN: 4810

European-Finnish (FIN) AF: 0.415 AC: 4380 AN: 10546

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26457 AN: 67918

Other (OTH) AF: 0.459 AC: 967 AN: 2108

Alfa AF: 0.408 Hom.: 25160

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.16
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1624802; hg19: chr12-130497472;