rs8107940

Positions:

• chr19-21454387-G-A

Variant summary

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

The ENST00000594557.1(ENSG00000268119):​n.2343C>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 0.216 in 151,460 control chromosomes in the GnomAD database, including 4,008 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 0.22 (4008 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000594557.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372321	XR_936422.3	n.375C>T		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000596705.5	n.379C>T		non_coding_transcript_exon_variant	3/4	4

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32677 AN: 151344 Hom.: 4014 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.209

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.216 AC: 32670 AN: 151460 Hom.: 4008 Cov.: 32 AF XY: 0.214 AC XY: 15849 AN XY: 73990

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.0789

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.205

Alfa AF: 0.232 Hom.: 579

Bravo AF: 0.214

Asia WGS AF: 0.132 AC: 460 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.12

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8107940; hg19: chr19-21637189;