rs7827900

Variant names:

• chr8-54356925-G-T
• rs7827900
• ENST00000772614.1:n.*107C>A

Variant summary

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

The ENST00000772614.1(ENSG00000300541):​n.*107C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0806 in 152,124 control chromosomes in the GnomAD database, including 633 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 0.081 (633 hom., cov: 33)
• Consequence: ENSG00000300541 ENST00000772614.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625
• Publications: 1 publications found

Genes affected

ENSG00000300541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 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
ENSG00000300541	ENST00000772614.1	n.*107C>A		downstream_gene_variant
ENSG00000300541	ENST00000772615.1	n.*135C>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0806 AC: 12246 AN: 152010 Hom.: 631 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0410

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0977

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0806 AC: 12263 AN: 152124 Hom.: 633 Cov.: 33 AF XY: 0.0828 AC XY: 6159 AN XY: 74352

African (AFR) AF: 0.121 AC: 5018 AN: 41500

American (AMR) AF: 0.117 AC: 1786 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0410 AC: 142 AN: 3466

East Asian (EAS) AF: 0.158 AC: 821 AN: 5182

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4820

European-Finnish (FIN) AF: 0.0977 AC: 1032 AN: 10564

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0456 AC: 3101 AN: 67988

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

Alfa AF: 0.0587 Hom.: 1561

Bravo AF: 0.0865

Asia WGS AF: 0.0890 AC: 310 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.64
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs7827900; hg19: chr8-55269485;