rs10485170

Positions:

• chr6-88172933-T-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: ENST00000624253.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000624253.1	n.673T>C		non_coding_transcript_exon_variant	1/1

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;