16-67674994-A-G

Variant names:

• chr16-67674994-A-G
• rs12449157
• NM_030819.4:c.*161T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 65 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GFOD2	NM_030819.4	c.*161T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000268797.12	NP_110446.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GFOD2	ENST00000268797.12	c.*161T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_030819.4	ENSP00000268797.7
GFOD2	ENST00000602522.1	n.2491T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
GFOD2	ENST00000602377.1	c.*997T>C		3_prime_UTR_variant	Exon 3 of 3	4		ENSP00000477784.1

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

African (AFR) AF: 0.635 AC: 9929 AN: 15644

American (AMR) AF: 0.211 AC: 4963 AN: 23508

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 2488 AN: 14870

East Asian (EAS) AF: 0.0349 AC: 1186 AN: 33972

South Asian (SAS) AF: 0.240 AC: 12413 AN: 51696

European-Finnish (FIN) AF: 0.181 AC: 5982 AN: 33002

Middle Eastern (MID) AF: 0.234 AC: 530 AN: 2264

European-Non Finnish (NFE) AF: 0.154 AC: 61387 AN: 398544

Other (OTH) AF: 0.194 AC: 6061 AN: 31292

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

African (AFR) AF: 0.632 AC: 26251 AN: 41516

American (AMR) AF: 0.228 AC: 3490 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3470

East Asian (EAS) AF: 0.0330 AC: 171 AN: 5184

South Asian (SAS) AF: 0.233 AC: 1123 AN: 4824

European-Finnish (FIN) AF: 0.189 AC: 2005 AN: 10618

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10558 AN: 68002

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.193 Hom.: 17685

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
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12449157; hg19: chr16-67708897;