rs5751761

Positions:

• chr22-23901549-C-T

Variant summary

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

The ENST00000609510.1(ENSG00000273295):​n.5520G>A 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 0.464 in 152,070 control chromosomes in the GnomAD database, including 17,788 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 0.46 (17788 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000273295 ENST00000609510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

Genes affected

ENSG00000273295 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23901549C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000273295	ENST00000609510.1	n.5520G>A		non_coding_transcript_exon_variant	1/1	6
ENSG00000290199	ENST00000703580.1	n.387-5439G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70529 AN: 151952 Hom.: 17775 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.465

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.464 AC: 70553 AN: 152070 Hom.: 17788 Cov.: 32 AF XY: 0.473 AC XY: 35128 AN XY: 74324

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.465

Alfa AF: 0.476 Hom.: 2872

Bravo AF: 0.446

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5751761; hg19: chr22-24243736;