10-114426623-T-C

Position:

• chr10-114426623-T-C

Variant summary

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

The ENST00000623755.1(ENSG00000279796):​n.776A>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 0.818 in 152,162 control chromosomes in the GnomAD database, including 51,168 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 0.82 (51167 hom., cov: 33)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: ENSG00000279796 ENST00000623755.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

Genes affected

ENSG00000279796 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.114426623T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279796	ENST00000623755.1	n.776A>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124315 AN: 152038 Hom.: 51146 Cov.: 33

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.839

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.818 AC: 124389 AN: 152156 Hom.: 51167 Cov.: 33 AF XY: 0.814 AC XY: 60577 AN XY: 74374

Gnomad4 AFR AF: 0.759

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.836

Alfa AF: 0.853 Hom.: 30557

Bravo AF: 0.815

Asia WGS AF: 0.708 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	13
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: rs6585278; hg19: chr10-116186382;