10-3011651-C-T

Variant summary

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

The ENST00000439575.2(ENSG00000234182):n.816C>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 0.269 in 149,446 control chromosomes in the GnomAD database, including 8,760 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 0.27 (8759 hom., cov: 28)
  • Exomes 𝑓: 0.21 (1 hom.)
• Consequence: ENST00000439575.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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
	ENST00000439575.2	n.816C>T		non_coding_transcript_exon_variant	2/3	2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40108 AN: 149314 Hom.: 8730 Cov.: 28

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.208 AC: 5 AN: 24 Hom.: 1 Cov.: 0 AF XY: 0.188 AC XY: 3 AN XY: 16

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.269 AC: 40184 AN: 149422 Hom.: 8759 Cov.: 28 AF XY: 0.263 AC XY: 19102 AN XY: 72700

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0608

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.243

Alfa AF: 0.196 Hom.: 598

Bravo AF: 0.287

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.8
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10751904; hg19: chr10-3053843;