ENST00000624219.1:n.5129A>C

Variant names:

• chr22-48057774-A-C
• rs117294
• ENST00000624219.1:n.5129A>C

Variant summary

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

The ENST00000624219.1(ENSG00000278890):​n.5129A>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 0.53 in 152,602 control chromosomes in the GnomAD database, including 21,756 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 0.53 (21674 hom., cov: 32)
  • Exomes 𝑓: 0.51 (82 hom.)
• Consequence: ENSG00000278890 ENST00000624219.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618
• Publications: 5 publications found

Genes affected

ENSG00000278890 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 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
ENSG00000278890	ENST00000624219.1	n.5129A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80600 AN: 151936 Hom.: 21654 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.510

GnomAD4 exome AF: 0.515 AC: 281 AN: 546 Hom.: 82 Cov.: 0 AF XY: 0.506 AC XY: 166 AN XY: 328

African (AFR) AF: 0.625 AC: 5 AN: 8

American (AMR) AF: 0.750 AC: 3 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.500 AC: 3 AN: 6

South Asian (SAS) AF: 0.00 AC: 0 AN: 6

European-Finnish (FIN) AF: 0.514 AC: 148 AN: 288

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.538 AC: 112 AN: 208

Other (OTH) AF: 0.364 AC: 8 AN: 22

GnomAD4 genome AF: 0.531 AC: 80668 AN: 152056 Hom.: 21674 Cov.: 32 AF XY: 0.528 AC XY: 39238 AN XY: 74312

African (AFR) AF: 0.578 AC: 23988 AN: 41492

American (AMR) AF: 0.554 AC: 8472 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3468

East Asian (EAS) AF: 0.507 AC: 2610 AN: 5144

South Asian (SAS) AF: 0.349 AC: 1679 AN: 4806

European-Finnish (FIN) AF: 0.527 AC: 5571 AN: 10580

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35063 AN: 67972

Other (OTH) AF: 0.512 AC: 1080 AN: 2108

Alfa AF: 0.508 Hom.: 50520

Bravo AF: 0.541

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.64
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs117294; hg19: chr22-48453591;