chr8-13629397-C-A

Variant names:

• chr8-13629397-C-A
• rs7006666
• ENST00000668622.2:n.-228C>A

Variant summary

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

The ENST00000668622.2(ENSG00000286798):​n.-228C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,174 control chromosomes in the GnomAD database, including 12,830 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 0.41 (12830 hom., cov: 31)
• Consequence: ENSG00000286798 ENST00000668622.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 3 publications found

Genes affected

ENSG00000286798 (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 (AFR) allele frequency at 95% confidence interval = 0.502 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
ENSG00000286798	ENST00000668622.2	n.-228C>A		upstream_gene_variant
ENSG00000286798	ENST00000811223.1	n.-240C>A		upstream_gene_variant
ENSG00000286798	ENST00000811224.1	n.-247C>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61393 AN: 151054 Hom.: 12820 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.406 AC: 61449 AN: 151174 Hom.: 12830 Cov.: 31 AF XY: 0.405 AC XY: 29909 AN XY: 73816

African (AFR) AF: 0.508 AC: 20919 AN: 41214

American (AMR) AF: 0.289 AC: 4372 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1347 AN: 3460

East Asian (EAS) AF: 0.434 AC: 2219 AN: 5114

South Asian (SAS) AF: 0.412 AC: 1969 AN: 4774

European-Finnish (FIN) AF: 0.380 AC: 3932 AN: 10360

Middle Eastern (MID) AF: 0.403 AC: 117 AN: 290

European-Non Finnish (NFE) AF: 0.375 AC: 25422 AN: 67852

Other (OTH) AF: 0.378 AC: 791 AN: 2094

Alfa AF: 0.378 Hom.: 45624

Bravo AF: 0.402

Asia WGS AF: 0.399 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs7006666; hg19: chr8-13486906;