22-28815390-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000272858 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607919.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272858	ENST00000607919.1	TSL:6	n.477C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000226471	ENST00000418292.1	TSL:3	n.34+14653C>T		intron	N/A
	ENSG00000226471	ENST00000451486.5	TSL:5	n.104-6582C>T		intron	N/A

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.909 AC: 20 AN: 22

Other (OTH) AF: 1.00 AC: 4 AN: 4

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0385499), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.984 AC: 40891 AN: 41560

American (AMR) AF: 0.968 AC: 14795 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3423 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5176

South Asian (SAS) AF: 0.998 AC: 4814 AN: 4824

European-Finnish (FIN) AF: 0.962 AC: 10213 AN: 10618

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.944 AC: 64242 AN: 68026

Other (OTH) AF: 0.966 AC: 2039 AN: 2110

Alfa AF: 0.953 Hom.: 43984

Bravo AF: 0.967

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.86
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs133440; hg19: chr22-29211378;