rs5760176

Positions:

• chr22-24005875-G-A
• chr22-24005875-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The XR_001755457.1(LOC105372959):​n.200G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.37 (769 hom., cov: 35)
  • Failed GnomAD Quality Control
• Consequence: LOC105372959 XR_001755457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

Genes affected

LOC105372959 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372959	XR_001755457.1	n.200G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.00 AC: 47913 AN: 129072 Hom.: 768 Cov.: 35 FAILED QC

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.379

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.371 AC: 47920 AN: 129144 Hom.: 769 Cov.: 35 AF XY: 0.373 AC XY: 23661 AN XY: 63420

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.378

Alfa AF: 0.372 Hom.: 2111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5760176; hg19: chr22-24402321;