rs5765558

Positions:

• chr22-45647099-A-G

Variant summary

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

The XR_001755590.2(LOC105373069):​n.157-2540A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,098 control chromosomes in the GnomAD database, including 12,798 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 0.41 (12798 hom., cov: 32)
• Consequence: LOC105373069 XR_001755590.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

Genes affected

LOC105373069 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373069	XR_001755590.2	n.157-2540A>G		intron_variant, non_coding_transcript_variant
LOC105373069	XR_007068130.1	n.600A>G		non_coding_transcript_exon_variant	2/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61965 AN: 151980 Hom.: 12781 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.408 AC: 62006 AN: 152098 Hom.: 12798 Cov.: 32 AF XY: 0.410 AC XY: 30460 AN XY: 74370

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.400

Alfa AF: 0.390 Hom.: 16112

Bravo AF: 0.412

Asia WGS AF: 0.439 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5765558; hg19: chr22-46042979;