10-87658973-C-A

Variant names:

• chr10-87658973-C-A
• rs2180968
• ENST00000438082.1:n.189C>A

Variant summary

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

The ENST00000438082.1(ENSG00000225913):​n.189C>A 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 0.337 in 152,224 control chromosomes in the GnomAD database, including 9,069 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 0.34 (9061 hom., cov: 33)
  • Exomes 𝑓: 0.33 (8 hom.)
• Consequence: ENSG00000225913 ENST00000438082.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

Genes affected

ENSG00000225913 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 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
ENSG00000225913	ENST00000438082.1	n.189C>A		non_coding_transcript_exon_variant	Exon 4 of 4	3
ENSG00000196566	ENST00000354527.2	n.146+885G>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51191 AN: 151958 Hom.: 9057 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.338

GnomAD4 exome AF: 0.331 AC: 49 AN: 148 Hom.: 8 Cov.: 0 AF XY: 0.340 AC XY: 36 AN XY: 106

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.250

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.339

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.337 AC: 51224 AN: 152076 Hom.: 9061 Cov.: 33 AF XY: 0.327 AC XY: 24327 AN XY: 74356

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0784

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.336

Alfa AF: 0.259 Hom.: 895

Bravo AF: 0.336

Asia WGS AF: 0.182 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.53
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2180968; hg19: chr10-89418730;