rs7929521

Variant names:

• chr11-20573237-G-A
• rs7929521
• XR_931105.1:n.-239C>T

Variant summary

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

The XR_931105.1(LOC105376584):​n.-239C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,988 control chromosomes in the GnomAD database, including 16,542 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 0.45 (16542 hom., cov: 32)
• Consequence: LOC105376584 XR_931105.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 2 publications found

Genes affected

LOC105376584 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 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: 0.449 AC: 68263 AN: 151868 Hom.: 16499 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.450 AC: 68366 AN: 151988 Hom.: 16542 Cov.: 32 AF XY: 0.442 AC XY: 32815 AN XY: 74260

African (AFR) AF: 0.648 AC: 26853 AN: 41448

American (AMR) AF: 0.380 AC: 5796 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1539 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1810 AN: 5154

South Asian (SAS) AF: 0.328 AC: 1581 AN: 4822

European-Finnish (FIN) AF: 0.324 AC: 3418 AN: 10536

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26001 AN: 67970

Other (OTH) AF: 0.411 AC: 866 AN: 2108

Alfa AF: 0.403 Hom.: 54993

Bravo AF: 0.466

Asia WGS AF: 0.357 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7929521; hg19: chr11-20594783;