XR_007067875.1:n.1022A>G

Variant names:

• chr21-42358786-A-G
• rs1547374
• XR_007067875.1:n.1022A>G

Variant summary

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

The XR_007067875.1(LOC105372815):​n.1022A>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 0.323 in 152,004 control chromosomes in the GnomAD database, including 8,165 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 0.32 (8165 hom., cov: 32)
• Consequence: LOC105372815 XR_007067875.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.749
• Publications: 29 publications found

Genes affected

LOC105372815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49030 AN: 151886 Hom.: 8143 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.323 AC: 49104 AN: 152004 Hom.: 8165 Cov.: 32 AF XY: 0.322 AC XY: 23894 AN XY: 74298

African (AFR) AF: 0.327 AC: 13556 AN: 41416

American (AMR) AF: 0.368 AC: 5624 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1482 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2371 AN: 5172

South Asian (SAS) AF: 0.312 AC: 1499 AN: 4812

European-Finnish (FIN) AF: 0.226 AC: 2389 AN: 10572

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21140 AN: 67970

Other (OTH) AF: 0.353 AC: 746 AN: 2114

Alfa AF: 0.322 Hom.: 37209

Bravo AF: 0.334

Asia WGS AF: 0.379 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.41
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs1547374; hg19: chr21-43778895;