chr6-127329221-C-G

Position:

• chr6-127329221-C-G

Variant summary

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

The NM_001002030.2(ECHDC1):​c.220+1588G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 151,712 control chromosomes in the GnomAD database, including 390 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 0.070 (390 hom., cov: 32)
• Consequence: ECHDC1 NM_001002030.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

ECHDC1 (HGNC:21489): (ethylmalonyl-CoA decarboxylase 1) Predicted to enable carboxy-lyase activity and enoyl-CoA hydratase activity. Predicted to be involved in fatty acid beta-oxidation. Predicted to be integral component of membrane. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ECHDC1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.09 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ECHDC1	NM_001002030.2	c.220+1588G>C		intron_variant		ENST00000454859.8	NP_001002030.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ECHDC1	ENST00000454859.8	c.220+1588G>C		intron_variant		1	NM_001002030.2	ENSP00000401751.3

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10555 AN: 151596 Hom.: 386 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0532

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.0966

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0706

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

GnomAD4 genome AF: 0.0697 AC: 10577 AN: 151712 Hom.: 390 Cov.: 32 AF XY: 0.0687 AC XY: 5095 AN XY: 74124

Gnomad4 AFR AF: 0.0805

Gnomad4 AMR AF: 0.0531

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.0973

Gnomad4 FIN AF: 0.0557

Gnomad4 NFE AF: 0.0668

Gnomad4 OTH AF: 0.0722

Alfa AF: 0.0198 Hom.: 12

Bravo AF: 0.0692

Asia WGS AF: 0.0920 AC: 318 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.012
DANN	Benign	0.56

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

Publications

LitVar

Other links and lift over

dbSNP: rs17054536; hg19: chr6-127650366;