rs117294

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr22-48057774-A-C
• chr22-48057774-A-G
• chr22-48057774-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000278890 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR exome AF: 0.625

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.514

Gnomad4 NFE exome AF: 0.538

Gnomad4 OTH exome AF: 0.364

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

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.512

Alfa AF: 0.503 Hom.: 35532

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs117294; hg19: chr22-48453591;