ENST00000624253.1:n.673T>C

Variant names:

• chr6-88172933-T-C
• rs10485170
• ENST00000624253.1:n.673T>C

Variant summary

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

The ENST00000624253.1(ENSG00000279565):​n.673T>C 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 0.141 in 152,220 control chromosomes in the GnomAD database, including 2,011 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 0.14 (2011 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000279565 ENST00000624253.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

Genes affected

ENSG00000279565 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279565	ENST00000624253.1	n.673T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21468 AN: 152102 Hom.: 2009 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.121

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

GnomAD4 genome AF: 0.141 AC: 21485 AN: 152220 Hom.: 2011 Cov.: 32 AF XY: 0.138 AC XY: 10311 AN XY: 74452

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.0921

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0800

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.0990

Gnomad4 OTH AF: 0.120

Alfa AF: 0.102 Hom.: 1799

Bravo AF: 0.146

Asia WGS AF: 0.0650 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485170; hg19: chr6-88882652;