rs5765558

Variant names:

• chr22-45647099-A-G
• rs5765558
• XR_007068130.1:n.600A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007068130.1(LOC105373069):​n.600A>G 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 0.408 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_007068130.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 5 publications found

Genes affected

LOC105373069 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105373069	XR_007068130.1	n.600A>G		non_coding_transcript_exon_variant	Exon 2 of 4
LOC105373069	XR_001755590.2	n.157-2540A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307862	ENST00000829473.1	n.162+991A>G		intron_variant	Intron 1 of 2
ENSG00000307862	ENST00000829474.1	n.933-48A>G		intron_variant	Intron 5 of 5
ENSG00000307862	ENST00000829475.1	n.388-48A>G		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.434 AC: 18019 AN: 41506

American (AMR) AF: 0.420 AC: 6414 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3468

East Asian (EAS) AF: 0.499 AC: 2571 AN: 5154

South Asian (SAS) AF: 0.347 AC: 1676 AN: 4828

European-Finnish (FIN) AF: 0.414 AC: 4386 AN: 10594

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26393 AN: 67956

Other (OTH) AF: 0.400 AC: 844 AN: 2110

Alfa AF: 0.392 Hom.: 20478

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
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs5765558; hg19: chr22-46042979;