rs2296090

Positions:

• chr20-48383513-A-C
• chr20-48383513-A-T

Variant summary

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

The ENST00000446280.1(ENSG00000236874):​n.257-43T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 145,566 control chromosomes in the GnomAD database, including 2,624 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 0.16 (2624 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000446280.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000446280.1	n.257-43T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23027 AN: 145458 Hom.: 2618 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.0998

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0948

Gnomad NFE AF: 0.0838

Gnomad OTH AF: 0.135

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.158 AC: 23063 AN: 145566 Hom.: 2624 Cov.: 32 AF XY: 0.157 AC XY: 11164 AN XY: 71290

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0771

Gnomad4 SAS AF: 0.0990

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.0838

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0900 Hom.: 511

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2296090; hg19: chr20-47012256;