12-132602515-C-T

Variant names:

• chr12-132602515-C-T
• rs4242909
• ENST00000738835.1:n.425G>A

Variant summary

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

The ENST00000738835.1(ENSG00000296413):​n.425G>A 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 0.552 in 152,002 control chromosomes in the GnomAD database, including 23,334 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 0.55 (23334 hom., cov: 32)
• Consequence: ENSG00000296413 ENST00000738835.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 9 publications found

Genes affected

ENSG00000296413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 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
ENSG00000296413	ENST00000738835.1	n.425G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83865 AN: 151884 Hom.: 23317 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.552 AC: 83917 AN: 152002 Hom.: 23334 Cov.: 32 AF XY: 0.553 AC XY: 41078 AN XY: 74286

African (AFR) AF: 0.525 AC: 21763 AN: 41422

American (AMR) AF: 0.583 AC: 8926 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3468

East Asian (EAS) AF: 0.794 AC: 4113 AN: 5178

South Asian (SAS) AF: 0.617 AC: 2974 AN: 4824

European-Finnish (FIN) AF: 0.508 AC: 5349 AN: 10536

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.546 AC: 37103 AN: 67960

Other (OTH) AF: 0.563 AC: 1186 AN: 2106

Alfa AF: 0.536 Hom.: 13483

Bravo AF: 0.558

Asia WGS AF: 0.676 AC: 2348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4242909; hg19: chr12-133179101;