chr6-32007374-T-G

Position:

• chr6-32007374-T-G

Variant summary

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

The ENST00000342991.10(ENSG00000290788):​n.1274T>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 0.218 in 1,341,104 control chromosomes in the GnomAD database, including 90,030 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 0.32 (11437 hom., cov: 26)
  • Exomes 𝑓: 0.21 (78593 hom.)
• Consequence: ENSG00000290788 ENST00000342991.10 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

ENSG00000290788 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP21A1P	NR_040090.1	n.1274T>G		non_coding_transcript_exon_variant	5/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290788	ENST00000342991.10	n.1274T>G		non_coding_transcript_exon_variant	5/8	3
CYP21A1P	ENST00000354927.4	n.836T>G		non_coding_transcript_exon_variant	7/10	6

Frequencies

GnomAD3 genomes AF: 0.324 AC: 44500 AN: 137376 Hom.: 11424 Cov.: 26

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.340

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.359

GnomAD3 exomes AF: 0.253 AC: 56949 AN: 225024 Hom.: 15165 AF XY: 0.261 AC XY: 32075 AN XY: 122742

Gnomad AFR exome AF: 0.565

Gnomad AMR exome AF: 0.180

Gnomad ASJ exome AF: 0.201

Gnomad EAS exome AF: 0.195

Gnomad SAS exome AF: 0.431

Gnomad FIN exome AF: 0.133

Gnomad NFE exome AF: 0.223

Gnomad OTH exome AF: 0.253

GnomAD4 exome AF: 0.206 AC: 248476 AN: 1203630 Hom.: 78593 Cov.: 38 AF XY: 0.213 AC XY: 127899 AN XY: 601202

Gnomad4 AFR exome AF: 0.572

Gnomad4 AMR exome AF: 0.173

Gnomad4 ASJ exome AF: 0.208

Gnomad4 EAS exome AF: 0.214

Gnomad4 SAS exome AF: 0.421

Gnomad4 FIN exome AF: 0.134

Gnomad4 NFE exome AF: 0.181

Gnomad4 OTH exome AF: 0.242

GnomAD4 genome AF: 0.324 AC: 44544 AN: 137474 Hom.: 11437 Cov.: 26 AF XY: 0.320 AC XY: 21427 AN XY: 67016

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.355

Alfa AF: 0.283 Hom.: 1748

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	18
DANN	Benign	0.90
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41315836; hg19: chr6-31975151; COSMIC: COSV61589954;