rs511996

Variant names:

• chr6-13405858-A-C
• rs511996
• NM_018988.4:c.254-40196T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-13405858-A-C
• chr6-13405858-A-G
• chr6-13405858-A-T

Variant summary

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

The NM_018988.4(GFOD1):​c.254-40196T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,028 control chromosomes in the GnomAD database, including 54,210 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 0.83 (54210 hom., cov: 30)
• Consequence: GFOD1 NM_018988.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GFOD1	NM_018988.4	c.254-40196T>G		intron_variant	Intron 1 of 1	ENST00000379287.4	NP_061861.1
GFOD1	NM_001242628.2	c.-56-40196T>G		intron_variant	Intron 1 of 1		NP_001229557.1
GFOD1	NM_001242630.2	c.-57+2052T>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.254-40196T>G		intron_variant	Intron 1 of 1	1	NM_018988.4	ENSP00000368589.3
GFOD1	ENST00000379284.1	c.-57+2052T>G		intron_variant	Intron 1 of 1	2		ENSP00000368586.1
GFOD1	ENST00000612338.4	c.-56-40196T>G		intron_variant	Intron 1 of 1	2		ENSP00000479493.1

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125458 AN: 151910 Hom.: 54200 Cov.: 30

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.826 AC: 125507 AN: 152028 Hom.: 54210 Cov.: 30 AF XY: 0.829 AC XY: 61613 AN XY: 74330

African (AFR) AF: 0.541 AC: 22402 AN: 41378

American (AMR) AF: 0.910 AC: 13903 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2878 AN: 3470

East Asian (EAS) AF: 0.930 AC: 4794 AN: 5156

South Asian (SAS) AF: 0.860 AC: 4147 AN: 4820

European-Finnish (FIN) AF: 0.949 AC: 10065 AN: 10610

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64419 AN: 68002

Other (OTH) AF: 0.842 AC: 1775 AN: 2108

Alfa AF: 0.913 Hom.: 30617

Bravo AF: 0.812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.38
PhyloP100		-0.57
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: rs511996; hg19: chr6-13406090;