rs10489068

Positions:

• chr4-10285644-A-G
• chr4-10285644-A-T

Variant summary

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

The ENST00000506077.1(ENSG00000250505):​n.65T>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 0.631 in 152,112 control chromosomes in the GnomAD database, including 30,654 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 0.63 (30629 hom., cov: 32)
  • Exomes 𝑓: 0.72 (25 hom.)
• Consequence: ENST00000506077.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 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
	ENST00000506077.1	n.65T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95793 AN: 151890 Hom.: 30609 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.623

GnomAD4 exome AF: 0.721 AC: 75 AN: 104 Hom.: 25 Cov.: 0 AF XY: 0.729 AC XY: 51 AN XY: 70

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.721

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.631 AC: 95862 AN: 152008 Hom.: 30629 Cov.: 32 AF XY: 0.632 AC XY: 46962 AN XY: 74308

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.618

Alfa AF: 0.608 Hom.: 3205

Bravo AF: 0.616

Asia WGS AF: 0.634 AC: 2204 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489068; hg19: chr4-10287268;