22-27020862-T-C

Variant names:

• chr22-27020862-T-C
• rs4417
• ENST00000623027.1:n.1494T>C

Variant summary

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

The ENST00000623027.1(ENSG00000279440):​n.1494T>C 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 0.858 in 151,982 control chromosomes in the GnomAD database, including 56,188 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 0.86 (56180 hom., cov: 29)
  • Exomes 𝑓: 0.94 (8 hom.)
• Consequence: ENSG00000279440 ENST00000623027.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

ENSG00000279440 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 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
ENSG00000279440	ENST00000623027.1	n.1494T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130218 AN: 151846 Hom.: 56130 Cov.: 29

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.864

GnomAD4 exome AF: 0.944 AC: 17 AN: 18 Hom.: 8 Cov.: 0 AF XY: 1.00 AC XY: 14 AN XY: 14

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.917

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.858 AC: 130332 AN: 151964 Hom.: 56180 Cov.: 29 AF XY: 0.855 AC XY: 63509 AN XY: 74286

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.841

Gnomad4 OTH AF: 0.864

Alfa AF: 0.842 Hom.: 45398

Bravo AF: 0.856

Asia WGS AF: 0.765 AC: 2661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4417; hg19: chr22-27416825;