12-10614199-A-G

Variant names:

• chr12-10614199-A-G
• rs2219383
• ENST00000790609.1:n.114A>G

Variant summary

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

The ENST00000790609.1(ENSG00000302947):​n.114A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,020 control chromosomes in the GnomAD database, including 40,997 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 (40997 hom., cov: 31)
• Consequence: ENSG00000302947 ENST00000790609.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 7 publications found

Genes affected

ENSG00000302947 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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
ENSG00000302947	ENST00000790609.1	n.114A>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000302947	ENST00000790608.1	n.258+304A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109240 AN: 151902 Hom.: 40966 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.719 AC: 109320 AN: 152020 Hom.: 40997 Cov.: 31 AF XY: 0.723 AC XY: 53745 AN XY: 74318

African (AFR) AF: 0.490 AC: 20278 AN: 41416

American (AMR) AF: 0.815 AC: 12462 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2567 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5134 AN: 5172

South Asian (SAS) AF: 0.824 AC: 3975 AN: 4824

European-Finnish (FIN) AF: 0.817 AC: 8627 AN: 10556

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53722 AN: 67994

Other (OTH) AF: 0.742 AC: 1559 AN: 2100

Alfa AF: 0.775 Hom.: 76903

Bravo AF: 0.710

Asia WGS AF: 0.888 AC: 3089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.2
DANN	Benign	0.79
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2219383; hg19: chr12-10766798;