1-237941595-C-T

Position:

• chr1-237941595-C-T

Variant summary

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

The ENST00000636511.1(ENSG00000283166):​n.898G>A 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 0.533 in 151,882 control chromosomes in the GnomAD database, including 22,418 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 0.53 (22418 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000283166 ENST00000636511.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

Genes affected

ENSG00000283166 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MTND2P27		n.237941595C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000283166	ENST00000636511.1	n.898G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80888 AN: 151764 Hom.: 22382 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.499

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.533 AC: 80970 AN: 151882 Hom.: 22418 Cov.: 32 AF XY: 0.539 AC XY: 40003 AN XY: 74216

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.500

Alfa AF: 0.403 Hom.: 1729

Bravo AF: 0.531

Asia WGS AF: 0.584 AC: 2027 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2499601; hg19: chr1-238104895;