chr10-86755315-T-C

Position:

• chr10-86755315-T-C

Variant summary

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

The ENST00000608826.1(ENSG00000272631):​n.984A>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 0.29 in 152,130 control chromosomes in the GnomAD database, including 7,675 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 0.29 (7673 hom., cov: 33)
  • Exomes 𝑓: 0.70 (2 hom.)
• Consequence: ENST00000608826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 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
	ENST00000608826.1	n.984A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44079 AN: 152002 Hom.: 7672 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.294

GnomAD4 exome AF: 0.700 AC: 7 AN: 10 Hom.: 2 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.290 AC: 44087 AN: 152120 Hom.: 7673 Cov.: 33 AF XY: 0.297 AC XY: 22057 AN XY: 74344

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.292

Alfa AF: 0.328 Hom.: 13474

Bravo AF: 0.279

Asia WGS AF: 0.437 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3905377; hg19: chr10-88515072;