22-28815390-C-T

Variant names:

• chr22-28815390-C-T
• rs133440
• ENST00000607919.1:n.477C>T

Variant summary

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

The ENST00000607919.1(ENSG00000272858):​n.477C>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 0.964 in 152,302 control chromosomes in the GnomAD database, including 70,759 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 0.96 (70746 hom., cov: 32)
  • Exomes 𝑓: 0.93 (13 hom.)
• Consequence: ENSG00000272858 ENST00000607919.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

Genes affected

ENSG00000272858 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272858	ENST00000607919.1	n.477C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000226471	ENST00000418292.1	n.34+14653C>T		intron_variant	Intron 1 of 1	3
ENSG00000226471	ENST00000451486.5	n.104-6582C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.964 AC: 146624 AN: 152154 Hom.: 70689 Cov.: 32

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.944

Gnomad OTH AF: 0.966

GnomAD4 exome AF: 0.933 AC: 28 AN: 30 Hom.: 13 Cov.: 0 AF XY: 0.955 AC XY: 21 AN XY: 22

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.909

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.964 AC: 146740 AN: 152272 Hom.: 70746 Cov.: 32 AF XY: 0.966 AC XY: 71883 AN XY: 74438

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.968

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.998

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.944

Gnomad4 OTH AF: 0.966

Alfa AF: 0.953 Hom.: 20910

Bravo AF: 0.967

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
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: rs133440; hg19: chr22-29211378;