rs2180968

Positions:

• chr10-87658973-C-A
• chr10-87658973-C-G

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: ENST00000438082.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000438082.1	n.189C>A		non_coding_transcript_exon_variant	4/4	3
	ENST00000354527.2	n.146+885G>T		intron_variant, non_coding_transcript_variant		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;