rs5017082

Variant names:

• chr12-38920762-C-A
• rs5017082
• ENST00000751277.1:n.219G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-38920762-C-A
• chr12-38920762-C-T

Variant summary

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

The ENST00000751277.1(ENSG00000297822):​n.219G>T 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 0.539 in 151,990 control chromosomes in the GnomAD database, including 25,196 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 0.54 (25196 hom., cov: 32)
• Consequence: ENSG00000297822 ENST00000751277.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 3 publications found

Genes affected

ENSG00000297822 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751277.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297822	ENST00000751277.1		n.219G>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81784 AN: 151872 Hom.: 25129 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.539 AC: 81918 AN: 151990 Hom.: 25196 Cov.: 32 AF XY: 0.535 AC XY: 39755 AN XY: 74278

African (AFR) AF: 0.860 AC: 35719 AN: 41524

American (AMR) AF: 0.463 AC: 7059 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1337 AN: 3466

East Asian (EAS) AF: 0.459 AC: 2366 AN: 5160

South Asian (SAS) AF: 0.369 AC: 1777 AN: 4822

European-Finnish (FIN) AF: 0.453 AC: 4776 AN: 10554

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27497 AN: 67902

Other (OTH) AF: 0.484 AC: 1019 AN: 2106

Alfa AF: 0.359 Hom.: 1446

Bravo AF: 0.559

Asia WGS AF: 0.454 AC: 1578 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.30
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs5017082; hg19: chr12-39314564;