chr6-127317203-A-T

Position:

• chr6-127317203-A-T

Variant summary

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

The NM_001002030.2(ECHDC1):​c.364-701T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 151,866 control chromosomes in the GnomAD database, including 40,708 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 0.73 (40708 hom., cov: 32)
• Consequence: ECHDC1 NM_001002030.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

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]

LOC105377994 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ECHDC1	NM_001002030.2	c.364-701T>A		intron_variant		ENST00000454859.8	NP_001002030.1
LOC105377994	XR_001744333.2	n.219A>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ECHDC1	ENST00000454859.8	c.364-701T>A		intron_variant		1	NM_001002030.2	ENSP00000401751	P2

Frequencies

GnomAD3 genomes AF: 0.731 AC: 110896 AN: 151748 Hom.: 40682 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.731 AC: 110971 AN: 151866 Hom.: 40708 Cov.: 32 AF XY: 0.725 AC XY: 53808 AN XY: 74182

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.753

Alfa AF: 0.740 Hom.: 5197

Bravo AF: 0.734

Asia WGS AF: 0.687 AC: 2389 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.6
DANN	Benign	0.37

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: rs7776136; hg19: chr6-127638348;