10-86755315-T-C

Variant names:

• chr10-86755315-T-C
• rs3905377
• ENST00000608826.1:n.984A>G

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: ENSG00000272631 ENST00000608826.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.172

Genes affected

ENSG00000272631 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272631	ENST00000608826.1	n.984A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;