chr6-13370256-T-C

Variant names:

• chr6-13370256-T-C
• rs552655
• NM_018988.4:c.254-4594A>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.254-4594A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,052 control chromosomes in the GnomAD database, including 16,728 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 0.43 (16728 hom., cov: 31)
• Consequence: GFOD1 NM_018988.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GFOD1	NM_018988.4	c.254-4594A>G		intron_variant	Intron 1 of 1	ENST00000379287.4	NP_061861.1
GFOD1	NM_001242628.2	c.-56-4594A>G		intron_variant	Intron 1 of 1		NP_001229557.1
GFOD1	NM_001242630.2	c.-56-4594A>G		intron_variant	Intron 1 of 1		NP_001229559.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GFOD1	ENST00000379287.4	c.254-4594A>G		intron_variant	Intron 1 of 1	1	NM_018988.4	ENSP00000368589.3
GFOD1	ENST00000379284.1	c.-56-4594A>G		intron_variant	Intron 1 of 1	2		ENSP00000368586.1
GFOD1	ENST00000612338.4	c.-56-4594A>G		intron_variant	Intron 1 of 1	2		ENSP00000479493.1

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64831 AN: 151934 Hom.: 16719 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.426 AC: 64847 AN: 152052 Hom.: 16728 Cov.: 31 AF XY: 0.434 AC XY: 32255 AN XY: 74312

African (AFR) AF: 0.119 AC: 4945 AN: 41520

American (AMR) AF: 0.564 AC: 8622 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1952 AN: 3472

East Asian (EAS) AF: 0.674 AC: 3470 AN: 5152

South Asian (SAS) AF: 0.564 AC: 2711 AN: 4808

European-Finnish (FIN) AF: 0.552 AC: 5820 AN: 10544

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35754 AN: 67952

Other (OTH) AF: 0.457 AC: 964 AN: 2108

Alfa AF: 0.500 Hom.: 8747

Bravo AF: 0.416

Asia WGS AF: 0.562 AC: 1953 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	8.4
DANN	Benign	0.80
PhyloP100		0.15
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: rs552655; hg19: chr6-13370488;