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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376584	XR_931105.1	n.-239C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;