22-27020862-T-C

Position:

• chr22-27020862-T-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: ENST00000623027.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000623027.1	n.1494T>C		non_coding_transcript_exon_variant	1/1

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;