20-23656343-C-T

Position:

• chr20-23656343-C-T

Variant summary

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

The ENST00000450971.1(ENSG00000225056):​n.48G>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 0.834 in 152,302 control chromosomes in the GnomAD database, including 53,078 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 0.83 (53035 hom., cov: 34)
  • Exomes 𝑓: 0.82 (43 hom.)
• Consequence: ENST00000450971.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904965	XR_007067748.1	n.202G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000450971.1	n.48G>A		non_coding_transcript_exon_variant	1/2	2
	ENST00000652804.1	n.193C>T		non_coding_transcript_exon_variant	1/4
	ENST00000657240.1	n.119C>T		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126803 AN: 152068 Hom.: 52996 Cov.: 34

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.847

GnomAD4 exome AF: 0.822 AC: 97 AN: 118 Hom.: 43 Cov.: 0 AF XY: 0.780 AC XY: 64 AN XY: 82

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.813

Gnomad4 OTH exome AF: 0.800

GnomAD4 genome AF: 0.834 AC: 126901 AN: 152184 Hom.: 53035 Cov.: 34 AF XY: 0.834 AC XY: 62071 AN XY: 74384

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.849

Alfa AF: 0.830 Hom.: 24828

Bravo AF: 0.843

Asia WGS AF: 0.844 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2424590; hg19: chr20-23636980;