6-31272264-C-T

Variant summary

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

The ENST00000692808.1(ENSG00000288813):n.25C>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 0.512 in 398,996 control chromosomes in the GnomAD database, including 57,148 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 0.56 (21454 hom., cov: 20)
  • Exomes 𝑓: 0.49 (35694 hom.)
• Consequence: ENST00000692808.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692808.1	n.25C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 75687 AN: 136236 Hom.: 21451 Cov.: 20

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.554

GnomAD4 exome AF: 0.489 AC: 128496 AN: 262654 Hom.: 35694 AF XY: 0.492 AC XY: 67608 AN XY: 137502

Gnomad4 AFR exome AF: 0.405

Gnomad4 AMR exome AF: 0.481

Gnomad4 ASJ exome AF: 0.569

Gnomad4 EAS exome AF: 0.726

Gnomad4 SAS exome AF: 0.580

Gnomad4 FIN exome AF: 0.389

Gnomad4 NFE exome AF: 0.458

Gnomad4 OTH exome AF: 0.484

GnomAD4 genome AF: 0.555 AC: 75717 AN: 136342 Hom.: 21454 Cov.: 20 AF XY: 0.554 AC XY: 36432 AN XY: 65782

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.553

Alfa AF: 0.551 Hom.: 1734

Asia WGS AF: 0.638 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	11
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524094; hg19: chr6-31240041; COSMIC: COSV66119511; COSMIC: COSV66119511;