5-79140388-C-T

Position:

• chr5-79140388-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.505 in 151,936 control chromosomes in the GnomAD database, including 20,565 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 0.50 (20565 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.79140388C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DMGDH	ENST00000518707.1	n.129-19036G>A		intron_variant		2
DMGDH	ENST00000520388.5	n.229-19036G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76585 AN: 151818 Hom.: 20520 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.505 AC: 76691 AN: 151936 Hom.: 20565 Cov.: 32 AF XY: 0.511 AC XY: 37932 AN XY: 74272

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.500

Alfa AF: 0.413 Hom.: 13193

Bravo AF: 0.517

Asia WGS AF: 0.710 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1915706; hg19: chr5-78436211;