rs2095388

Variant names:

• chr10-13142045-A-G
• rs2095388
• ENST00000442900.1:n.*140T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-13142045-A-G
• chr10-13142045-A-T

Variant summary

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

The ENST00000442900.1(ENSG00000228330):​n.*140T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,058 control chromosomes in the GnomAD database, including 6,461 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 (6461 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000228330 ENST00000442900.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

Genes affected

ENSG00000228330 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.387 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
ENSG00000228330	ENST00000442900.1	n.*140T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43759 AN: 151938 Hom.: 6459 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.338

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.288 AC: 43785 AN: 152058 Hom.: 6461 Cov.: 32 AF XY: 0.287 AC XY: 21351 AN XY: 74330

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.336

Alfa AF: 0.281 Hom.: 2905

Bravo AF: 0.308

Asia WGS AF: 0.256 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2095388; hg19: chr10-13184045;