chr5-151687037-C-T

Position:

• chr5-151687037-C-T

Variant summary

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

The NR_109873.1(CLMAT3):​n.1100C>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 0.0422 in 153,708 control chromosomes in the GnomAD database, including 190 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 0.042 (189 hom., cov: 32)
  • Exomes 𝑓: 0.051 (1 hom.)
• Consequence: CLMAT3 NR_109873.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

CLMAT3 (HGNC:52287): (colorectal liver metastasis associated transcript 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.099 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLMAT3	NR_109873.1	n.1100C>T		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLMAT3	ENST00000510576.6	n.1100C>T		non_coding_transcript_exon_variant	5/5	1
CLMAT3	ENST00000518905.1	n.192+7701C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0422 AC: 6415 AN: 152136 Hom.: 190 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0522

GnomAD4 exome AF: 0.0509 AC: 74 AN: 1454 Hom.: 1 Cov.: 0 AF XY: 0.0535 AC XY: 52 AN XY: 972

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.100

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.111

Gnomad4 SAS exome AF: 0.100

Gnomad4 FIN exome AF: 0.0563

Gnomad4 NFE exome AF: 0.0461

Gnomad4 OTH exome AF: 0.0370

GnomAD4 genome AF: 0.0422 AC: 6419 AN: 152254 Hom.: 189 Cov.: 32 AF XY: 0.0440 AC XY: 3277 AN XY: 74448

Gnomad4 AFR AF: 0.0111

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.0431

Gnomad4 SAS AF: 0.0420

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.0460

Gnomad4 OTH AF: 0.0511

Alfa AF: 0.0444 Hom.: 24

Bravo AF: 0.0469

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.72

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: rs4958281; hg19: chr5-151066598;