10-114426623-T-C

Variant names:

• chr10-114426623-T-C
• rs6585278
• ENST00000623755.1:n.776A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000279796 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623755.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279796	ENST00000623755.1	TSL:6	n.776A>G		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.759 AC: 31468 AN: 41482

American (AMR) AF: 0.857 AC: 13112 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3105 AN: 3472

East Asian (EAS) AF: 0.557 AC: 2879 AN: 5170

South Asian (SAS) AF: 0.827 AC: 3976 AN: 4810

European-Finnish (FIN) AF: 0.790 AC: 8371 AN: 10600

Middle Eastern (MID) AF: 0.842 AC: 246 AN: 292

European-Non Finnish (NFE) AF: 0.863 AC: 58721 AN: 68006

Other (OTH) AF: 0.836 AC: 1769 AN: 2116

Alfa AF: 0.853 Hom.: 33647

Bravo AF: 0.815

Asia WGS AF: 0.708 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	13
DANN	Benign	0.90
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs6585278; hg19: chr10-116186382;