10-119081149-A-G

Position:

• chr10-119081149-A-G

Variant summary

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

The ENST00000687829.2(ENSG00000289126):​n.221A>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 0.401 in 985,192 control chromosomes in the GnomAD database, including 81,559 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 0.32 (8755 hom., cov: 33)
  • Exomes 𝑓: 0.42 (72804 hom.)
• Consequence: ENSG00000289126 ENST00000687829.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ENSG00000289126 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.119081149A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289126	ENST00000687829.2	n.221A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49279 AN: 151964 Hom.: 8754 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.415 AC: 345783 AN: 833110 Hom.: 72804 Cov.: 31 AF XY: 0.415 AC XY: 159848 AN XY: 384714

Gnomad4 AFR exome AF: 0.162

Gnomad4 AMR exome AF: 0.350

Gnomad4 ASJ exome AF: 0.315

Gnomad4 EAS exome AF: 0.417

Gnomad4 SAS exome AF: 0.309

Gnomad4 FIN exome AF: 0.417

Gnomad4 NFE exome AF: 0.425

Gnomad4 OTH exome AF: 0.382

GnomAD4 genome AF: 0.324 AC: 49291 AN: 152082 Hom.: 8755 Cov.: 33 AF XY: 0.323 AC XY: 23990 AN XY: 74352

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.307

Alfa AF: 0.357 Hom.: 1960

Bravo AF: 0.317

Asia WGS AF: 0.317 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.17
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: rs3824830; hg19: chr10-120840661;