3-43079537-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032806.6(POMGNT2):c.*152G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0064 in 663,854 control chromosomes in the GnomAD database, including 140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.020 (109 hom., cov: 33)
  • Exomes 𝑓: 0.0023 (31 hom.)
• Consequence: POMGNT2 NM_032806.6 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.488

Genes affected

POMGNT2 (HGNC:25902): (protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)) This gene encodes a protein with glycosyltransferase activity although its function is not currently known. [provided by RefSeq, Sep 2012]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 3-43079537-C-A is Benign according to our data. Variant chr3-43079537-C-A is described in ClinVar as [Benign]. Clinvar id is 1182260.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POMGNT2	NM_032806.6	c.*152G>T		3_prime_UTR_variant	2/2	ENST00000344697.3
POMGNT2	XM_005265515.4	c.*152G>T		3_prime_UTR_variant	3/3
POMGNT2	XM_011534163.3	c.*152G>T		3_prime_UTR_variant	3/3
POMGNT2	XM_017007353.2	c.*152G>T		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POMGNT2	ENST00000344697.3	c.*152G>T		3_prime_UTR_variant	2/2	1	NM_032806.6	P1

Frequencies

GnomAD3 genomes AF: 0.0202 AC: 3070 AN: 152146 Hom.: 109 Cov.: 33

Gnomad AFR AF: 0.0698

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00877

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.0143

GnomAD4 exome AF: 0.00230 AC: 1176 AN: 511590 Hom.: 31 Cov.: 6 AF XY: 0.00198 AC XY: 526 AN XY: 265904

Gnomad4 AFR exome AF: 0.0667

Gnomad4 AMR exome AF: 0.00566

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000222

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000973

Gnomad4 OTH exome AF: 0.00492

GnomAD4 genome AF: 0.0202 AC: 3072 AN: 152264 Hom.: 109 Cov.: 33 AF XY: 0.0197 AC XY: 1466 AN XY: 74452

Gnomad4 AFR AF: 0.0696

Gnomad4 AMR AF: 0.00876

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000162

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.000840 Hom.: 2

Bravo AF: 0.0236

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	4.3
Dann	Benign	0.63

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: rs78518984; hg19: chr3-43121029;