rs890950

Positions:

• chr5-34043960-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000382079.3(C1QTNF3-AMACR):​n.37-8202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,068 control chromosomes in the GnomAD database, including 5,022 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 0.25 (5019 hom., cov: 32)
  • Exomes 𝑓: 0.33 (3 hom.)
• Consequence: C1QTNF3-AMACR ENST00000382079.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

Genes affected

C1QTNF3-AMACR (HGNC:49198): (C1QTNF3-AMACR readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring C1q and tumor necrosis factor related protein 3 (C1QTNF3) and alpha-methylacyl-CoA racemase (AMACR) genes on chromosome 5. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus not likely to produce a protein product. [provided by RefSeq, Mar 2011]

C1QTNF3-AMACR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1QTNF3-AMACR	NR_037951.1	n.112-8202C>T		intron_variant
C1QTNF3	NR_146599.1	n.895-8202C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1QTNF3-AMACR	ENST00000382079.3	n.37-8202C>T		intron_variant		2		ENSP00000371511.3

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37294 AN: 151920 Hom.: 5005 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.284

GnomAD4 exome AF: 0.333 AC: 10 AN: 30 Hom.: 3 AF XY: 0.346 AC XY: 9 AN XY: 26

Gnomad4 AFR exome AF: 0.250

Gnomad4 SAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.350

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.245 AC: 37315 AN: 152038 Hom.: 5019 Cov.: 32 AF XY: 0.249 AC XY: 18521 AN XY: 74314

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.288

Alfa AF: 0.267 Hom.: 723

Bravo AF: 0.234

Asia WGS AF: 0.318 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.79
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs890950; hg19: chr5-34044065;