6-32006086-C-T

Position:

• chr6-32006086-C-T

Variant summary

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

The ENST00000342991.10(ENSG00000290788):​n.451C>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 0.454 in 1,282,454 control chromosomes in the GnomAD database, including 167,921 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 0.43 (17783 hom., cov: 27)
  • Exomes 𝑓: 0.46 (150138 hom.)
• Consequence: ENSG00000290788 ENST00000342991.10 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

ENSG00000290788 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP21A1P	NR_040090.1	n.451C>T		non_coding_transcript_exon_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290788	ENST00000342991.10	n.451C>T		non_coding_transcript_exon_variant	1/8	3
CYP21A1P	ENST00000354927.4	n.292+9C>T		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.433 AC: 61021 AN: 141078 Hom.: 17763 Cov.: 27

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.588

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.432

GnomAD3 exomes AF: 0.483 AC: 105323 AN: 218132 Hom.: 31928 AF XY: 0.479 AC XY: 56523 AN XY: 117964

Gnomad AFR exome AF: 0.322

Gnomad AMR exome AF: 0.605

Gnomad ASJ exome AF: 0.588

Gnomad EAS exome AF: 0.352

Gnomad SAS exome AF: 0.403

Gnomad FIN exome AF: 0.569

Gnomad NFE exome AF: 0.481

Gnomad OTH exome AF: 0.475

GnomAD4 exome AF: 0.457 AC: 521738 AN: 1141258 Hom.: 150138 Cov.: 20 AF XY: 0.458 AC XY: 264291 AN XY: 576938

Gnomad4 AFR exome AF: 0.307

Gnomad4 AMR exome AF: 0.590

Gnomad4 ASJ exome AF: 0.579

Gnomad4 EAS exome AF: 0.395

Gnomad4 SAS exome AF: 0.401

Gnomad4 FIN exome AF: 0.545

Gnomad4 NFE exome AF: 0.454

Gnomad4 OTH exome AF: 0.444

GnomAD4 genome AF: 0.433 AC: 61078 AN: 141196 Hom.: 17783 Cov.: 27 AF XY: 0.435 AC XY: 29880 AN XY: 68660

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.437

Alfa AF: 0.459 Hom.: 3429

Asia WGS AF: 0.428 AC: 1463 AN: 3414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.56
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28361033; hg19: chr6-31973863; COSMIC: COSV61590002;