20-23656343-C-T

Variant names:

• chr20-23656343-C-T
• rs2424590
• ENST00000450971.2:n.291G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000450971.2(ENSG00000225056):​n.291G>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: ENSG00000225056 ENST00000450971.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 10 publications found

Genes affected

ENSG00000225056 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450971.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225056	ENST00000450971.2	TSL:2	n.291G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000286117	ENST00000652804.1		n.193C>T		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000286117	ENST00000657240.2		n.270C>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.813 AC: 78 AN: 96

Other (OTH) AF: 0.800 AC: 8 AN: 10

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

African (AFR) AF: 0.791 AC: 32838 AN: 41512

American (AMR) AF: 0.900 AC: 13766 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2976 AN: 3472

East Asian (EAS) AF: 0.931 AC: 4812 AN: 5166

South Asian (SAS) AF: 0.738 AC: 3556 AN: 4820

European-Finnish (FIN) AF: 0.827 AC: 8767 AN: 10602

Middle Eastern (MID) AF: 0.870 AC: 254 AN: 292

European-Non Finnish (NFE) AF: 0.843 AC: 57292 AN: 67992

Other (OTH) AF: 0.849 AC: 1795 AN: 2114

Alfa AF: 0.831 Hom.: 27814

Bravo AF: 0.843

Asia WGS AF: 0.844 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.80
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2424590; hg19: chr20-23636980;