6-13457385-T-C

Variant names:

• chr6-13457385-T-C
• rs1863995
• NM_018988.4:c.253+29253A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018988.4(GFOD1):​c.253+29253A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,096 control chromosomes in the GnomAD database, including 44,623 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 0.76 (44623 hom., cov: 31)
• Consequence: GFOD1 NM_018988.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 3 publications found

Genes affected

GFOD1 (HGNC:21096): (Gfo/Idh/MocA-like oxidoreductase domain containing 1) Predicted to enable nucleotide binding activity and oxidoreductase activity. Predicted to be located in extracellular region. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GFOD1	NM_018988.4	c.253+29253A>G		intron_variant	Intron 1 of 1	ENST00000379287.4	NP_061861.1
GFOD1	NM_001242628.2	c.-57+28626A>G		intron_variant	Intron 1 of 1		NP_001229557.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GFOD1	ENST00000379287.4	c.253+29253A>G		intron_variant	Intron 1 of 1	1	NM_018988.4	ENSP00000368589.3
GFOD1	ENST00000612338.4	c.-57+28626A>G		intron_variant	Intron 1 of 1	2		ENSP00000479493.1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116047 AN: 151978 Hom.: 44585 Cov.: 31

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.788

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.764 AC: 116147 AN: 152096 Hom.: 44623 Cov.: 31 AF XY: 0.766 AC XY: 56970 AN XY: 74348

African (AFR) AF: 0.812 AC: 33672 AN: 41482

American (AMR) AF: 0.825 AC: 12628 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2838 AN: 3472

East Asian (EAS) AF: 0.830 AC: 4285 AN: 5162

South Asian (SAS) AF: 0.854 AC: 4124 AN: 4828

European-Finnish (FIN) AF: 0.689 AC: 7278 AN: 10560

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48681 AN: 67976

Other (OTH) AF: 0.787 AC: 1663 AN: 2112

Alfa AF: 0.736 Hom.: 21213

Bravo AF: 0.776

Asia WGS AF: 0.809 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.98
DANN	Benign	0.69
PhyloP100		-0.94
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: rs1863995; hg19: chr6-13457617;