12-5047109-A-G

Variant names:

• chr12-5047109-A-G
• rs1860420
• ENST00000823332.1:n.891T>C

Variant summary

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

The ENST00000823332.1(ENSG00000307076):​n.891T>C 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 0.624 in 152,048 control chromosomes in the GnomAD database, including 30,454 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 0.62 (30454 hom., cov: 32)
• Consequence: ENSG00000307076 ENST00000823332.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 1 publications found

Genes affected

ENSG00000307076 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 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
ENSG00000307076	ENST00000823332.1	n.891T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94764 AN: 151930 Hom.: 30424 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.624 AC: 94853 AN: 152048 Hom.: 30454 Cov.: 32 AF XY: 0.629 AC XY: 46719 AN XY: 74320

African (AFR) AF: 0.784 AC: 32524 AN: 41462

American (AMR) AF: 0.581 AC: 8893 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2109 AN: 3472

East Asian (EAS) AF: 0.686 AC: 3547 AN: 5168

South Asian (SAS) AF: 0.660 AC: 3172 AN: 4808

European-Finnish (FIN) AF: 0.619 AC: 6542 AN: 10566

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36279 AN: 67960

Other (OTH) AF: 0.590 AC: 1244 AN: 2110

Alfa AF: 0.563 Hom.: 63535

Bravo AF: 0.624

Asia WGS AF: 0.685 AC: 2383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.13
DANN	Benign	0.59
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1860420; hg19: chr12-5156275;