rs5751761

Variant names:

• chr22-23901549-C-T
• rs5751761
• ENST00000609510.1:n.5520G>A

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000273295	ENST00000609510.1	n.5520G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000290199	ENST00000703580.1	n.387-5439G>A		intron_variant	Intron 3 of 3

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;