rs12449157

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-67674994-A-C
• chr16-67674994-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_030819.4(GFOD2):​c.*161T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000165 in 605,496 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.000017 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000165 AC: 10 AN: 605496 Hom.: 0 Cov.: 8 AF XY: 0.0000158 AC XY: 5 AN XY: 315882

African (AFR) AF: 0.00 AC: 0 AN: 15666

American (AMR) AF: 0.00 AC: 0 AN: 23548

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14880

East Asian (EAS) AF: 0.00 AC: 0 AN: 33980

South Asian (SAS) AF: 0.00 AC: 0 AN: 51758

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 33020

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2264

European-Non Finnish (NFE) AF: 0.0000175 AC: 7 AN: 399044

Other (OTH) AF: 0.0000957 AC: 3 AN: 31336

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 17685

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.46
PhyloP100		-0.22

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;