XR_007062357.1:n.562G>A

Variant names:

• chr10-44577763-G-A
• rs1021055
• XR_007062357.1:n.562G>A

Variant summary

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

The XR_007062357.1(LOC124902533):​n.562G>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 0.411 in 152,010 control chromosomes in the GnomAD database, including 13,926 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 (13926 hom., cov: 32)
• Consequence: LOC124902533 XR_007062357.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 4 publications found

Genes affected

LOC124902533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62439 AN: 151892 Hom.: 13910 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.411 AC: 62495 AN: 152010 Hom.: 13926 Cov.: 32 AF XY: 0.415 AC XY: 30820 AN XY: 74276

African (AFR) AF: 0.233 AC: 9660 AN: 41480

American (AMR) AF: 0.490 AC: 7479 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1353 AN: 3462

East Asian (EAS) AF: 0.447 AC: 2308 AN: 5158

South Asian (SAS) AF: 0.511 AC: 2457 AN: 4810

European-Finnish (FIN) AF: 0.502 AC: 5289 AN: 10534

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32446 AN: 67976

Other (OTH) AF: 0.422 AC: 891 AN: 2112

Alfa AF: 0.451 Hom.: 9327

Bravo AF: 0.405

Asia WGS AF: 0.493 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.26
DANN	Benign	0.33
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1021055; hg19: chr10-45073211;