rs7828042

Variant names:

• chr8-142737965-A-G
• rs7828042
• ENST00000839249.1:n.-72A>G

Variant summary

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

The ENST00000839249.1(ENSG00000253196):​n.-72A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,886 control chromosomes in the GnomAD database, including 8,948 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 0.34 (8948 hom., cov: 33)
• Consequence: ENSG00000253196 ENST00000839249.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 9 publications found

Genes affected

ENSG00000253196 (HGNC:58427):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253196	ENST00000839249.1	n.-72A>G		upstream_gene_variant
ENSG00000253196	ENST00000839250.1	n.-225A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51169 AN: 151766 Hom.: 8937 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.337 AC: 51201 AN: 151886 Hom.: 8948 Cov.: 33 AF XY: 0.340 AC XY: 25197 AN XY: 74200

African (AFR) AF: 0.241 AC: 9993 AN: 41404

American (AMR) AF: 0.404 AC: 6173 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1203 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1479 AN: 5134

South Asian (SAS) AF: 0.353 AC: 1700 AN: 4820

European-Finnish (FIN) AF: 0.423 AC: 4463 AN: 10542

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25047 AN: 67908

Other (OTH) AF: 0.337 AC: 710 AN: 2106

Alfa AF: 0.357 Hom.: 15810

Bravo AF: 0.330

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7828042; hg19: chr8-143819383;