chr16-67674994-A-G

Position:

• chr16-67674994-A-G

Variant summary

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

The NM_030819.4(GFOD2):​c.*161T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 757,032 control chromosomes in the GnomAD database, including 21,830 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 0.30 (10137 hom., cov: 33)
  • Exomes 𝑓: 0.17 (11693 hom.)
• Consequence: GFOD2 NM_030819.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

Genes affected

GFOD2 (HGNC:28159): (Gfo/Idh/MocA-like oxidoreductase domain containing 2) Predicted to enable nucleotide binding activity and oxidoreductase activity. Predicted to be involved in extracellular matrix organization. Predicted to be located in extracellular region. Predicted to be active in extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

GFOD2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GFOD2	NM_030819.4	c.*161T>C		3_prime_UTR_variant	3/3	ENST00000268797.12	NP_110446.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GFOD2	ENST00000268797	c.*161T>C		3_prime_UTR_variant	3/3	1	NM_030819.4	ENSP00000268797.7
GFOD2	ENST00000602377	c.*997T>C		3_prime_UTR_variant	3/3	4		ENSP00000477784.1
GFOD2	ENST00000602522.1	n.2491T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44861 AN: 152122 Hom.: 10102 Cov.: 33

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0327

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.265

GnomAD4 exome AF: 0.174 AC: 104939 AN: 604792 Hom.: 11693 Cov.: 8 AF XY: 0.175 AC XY: 55070 AN XY: 315530

Gnomad4 AFR exome AF: 0.635

Gnomad4 AMR exome AF: 0.211

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.0349

Gnomad4 SAS exome AF: 0.240

Gnomad4 FIN exome AF: 0.181

Gnomad4 NFE exome AF: 0.154

Gnomad4 OTH exome AF: 0.194

GnomAD4 genome AF: 0.295 AC: 44946 AN: 152240 Hom.: 10137 Cov.: 33 AF XY: 0.293 AC XY: 21793 AN XY: 74446

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0330

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.266

Alfa AF: 0.169 Hom.: 5829

Bravo AF: 0.309

Asia WGS AF: 0.215 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.39

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: rs12449157; hg19: chr16-67708897;