6-166383344-C-G

Position:

• chr6-166383344-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000568025.1(MPC1-DT):​n.156C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 155,946 control chromosomes in the GnomAD database, including 34,193 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.64 (33095 hom., cov: 35)
  • Exomes 𝑓: 0.75 (1098 hom.)
• Consequence: MPC1-DT ENST00000568025.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.46

Genes affected

MPC1-DT (HGNC:55366): (MPC1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 6-166383344-C-G is Benign according to our data. Variant chr6-166383344-C-G is described in ClinVar as [Benign]. Clinvar id is 682624.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MPC1-DT	ENST00000568025.1	n.156C>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96649 AN: 151982 Hom.: 33084 Cov.: 35

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.670

GnomAD4 exome AF: 0.748 AC: 2885 AN: 3856 Hom.: 1098 Cov.: 0 AF XY: 0.759 AC XY: 1527 AN XY: 2012

Gnomad4 AFR exome AF: 0.369

Gnomad4 AMR exome AF: 0.736

Gnomad4 ASJ exome AF: 0.778

Gnomad4 EAS exome AF: 0.953

Gnomad4 SAS exome AF: 0.931

Gnomad4 FIN exome AF: 0.711

Gnomad4 NFE exome AF: 0.742

Gnomad4 OTH exome AF: 0.769

GnomAD4 genome AF: 0.636 AC: 96670 AN: 152090 Hom.: 33095 Cov.: 35 AF XY: 0.643 AC XY: 47847 AN XY: 74372

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.675

Alfa AF: 0.579 Hom.: 1872

Bravo AF: 0.623

Asia WGS AF: 0.891 AC: 3077 AN: 3456

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295338; hg19: chr6-166796832;