6-166383195-C-T

Position:

• chr6-166383195-C-T

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.7C>T 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 0.0107 in 360,334 control chromosomes in the GnomAD database, including 143 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.022 (128 hom., cov: 35)
  • Exomes 𝑓: 0.0023 (15 hom.)
• Consequence: MPC1-DT ENST00000568025.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.07

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=-0.75).
• BP6: Variant 6-166383195-C-T is Benign according to our data. Variant chr6-166383195-C-T is described in ClinVar as [Benign]. Clinvar id is 1237653.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0752 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.7C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0222 AC: 3382 AN: 152152 Hom.: 128 Cov.: 35

Gnomad AFR AF: 0.0775

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00785

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000827

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.0134

GnomAD4 exome AF: 0.00233 AC: 484 AN: 208076 Hom.: 15 Cov.: 0 AF XY: 0.00201 AC XY: 216 AN XY: 107248

Gnomad4 AFR exome AF: 0.0723

Gnomad4 AMR exome AF: 0.00622

Gnomad4 ASJ exome AF: 0.000283

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000865

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000980

Gnomad4 OTH exome AF: 0.00538

GnomAD4 genome AF: 0.0222 AC: 3384 AN: 152258 Hom.: 128 Cov.: 35 AF XY: 0.0210 AC XY: 1565 AN XY: 74446

Gnomad4 AFR AF: 0.0774

Gnomad4 AMR AF: 0.00784

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000235

Gnomad4 OTH AF: 0.0132

Alfa AF: 0.0125 Hom.: 8

Bravo AF: 0.0245

Asia WGS AF: 0.00232 AC: 9 AN: 3462

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

Jul 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.3
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs114147375; hg19: chr6-166796683;