rs928199

Positions:

• chr20-37678154-C-T

Variant summary

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

The ENST00000373508.2(ENSG00000204117):​n.377C>T 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 0.0985 in 152,848 control chromosomes in the GnomAD database, including 1,030 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 0.099 (1030 hom., cov: 32)
  • Exomes 𝑓: 0.080 (0 hom.)
• Consequence: ENSG00000204117 ENST00000373508.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

ENSG00000204117 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100287792	NR_040021.1	n.374C>T		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000204117	ENST00000373508.2	n.377C>T		non_coding_transcript_exon_variant	2/4	2
ENSG00000204117	ENST00000655861.1	n.199-186C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 15004 AN: 152158 Hom.: 1030 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0293

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.0775

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.106

GnomAD4 exome AF: 0.0804 AC: 46 AN: 572 Hom.: 0 Cov.: 0 AF XY: 0.0773 AC XY: 28 AN XY: 362

Gnomad4 AFR exome AF: 0.333

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0810

Gnomad4 NFE exome AF: 0.0727

Gnomad4 OTH exome AF: 0.0500

GnomAD4 genome AF: 0.0986 AC: 15017 AN: 152276 Hom.: 1030 Cov.: 32 AF XY: 0.0978 AC XY: 7283 AN XY: 74456

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0748

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.0293

Gnomad4 SAS AF: 0.0327

Gnomad4 FIN AF: 0.0775

Gnomad4 NFE AF: 0.0640

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0880 Hom.: 118

Bravo AF: 0.103

Asia WGS AF: 0.0410 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs928199; hg19: chr20-36306556;