rs117294

Positions:

• 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: ENST00000624219.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000624219.1	n.5129A>C		non_coding_transcript_exon_variant	1/1

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;