ENST00000566457.1:n.3139A>G

Variant names:

• chr8-22680871-T-C
• rs10104039
• ENST00000566457.1:n.3139A>G

Variant summary

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

The ENST00000566457.1(ENSG00000261026):​n.3139A>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 0.589 in 151,788 control chromosomes in the GnomAD database, including 26,635 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 0.59 (26627 hom., cov: 33)
  • Exomes 𝑓: 0.48 (8 hom.)
• Consequence: ENSG00000261026 ENST00000566457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

Genes affected

ENSG00000261026 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986924	XR_001745827.2	n.5481T>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261026	ENST00000566457.1	n.3139A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89308 AN: 151616 Hom.: 26605 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.596

GnomAD4 exome AF: 0.481 AC: 26 AN: 54 Hom.: 8 Cov.: 0 AF XY: 0.524 AC XY: 22 AN XY: 42

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.550

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.589 AC: 89363 AN: 151734 Hom.: 26627 Cov.: 33 AF XY: 0.593 AC XY: 44002 AN XY: 74192

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.590

Alfa AF: 0.605 Hom.: 37894

Bravo AF: 0.588

Asia WGS AF: 0.544 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10104039; hg19: chr8-22538384;