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. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000228330 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.281 AC: 11646 AN: 41478

American (AMR) AF: 0.396 AC: 6038 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1563 AN: 5170

South Asian (SAS) AF: 0.242 AC: 1167 AN: 4814

European-Finnish (FIN) AF: 0.211 AC: 2236 AN: 10582

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18992 AN: 67966

Other (OTH) AF: 0.336 AC: 708 AN: 2108

Alfa AF: 0.282 Hom.: 3229

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
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs2095388; hg19: chr10-13184045;