4-122825787-C-G

Variant names:

• chr4-122825787-C-G
• rs308395
• ENST00000779266.1:n.*249C>G

Variant summary

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

The ENST00000779266.1(ENSG00000301488):​n.*249C>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,136 control chromosomes in the GnomAD database, including 10,747 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 0.30 (10747 hom., cov: 32)
• Consequence: ENSG00000301488 ENST00000779266.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 18 publications found

Genes affected

ENSG00000301488 (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 = 0.647 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
ENSG00000301488	ENST00000779266.1	n.*249C>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45484 AN: 152018 Hom.: 10706 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.300 AC: 45586 AN: 152136 Hom.: 10747 Cov.: 32 AF XY: 0.297 AC XY: 22106 AN XY: 74392

African (AFR) AF: 0.653 AC: 27111 AN: 41490

American (AMR) AF: 0.243 AC: 3720 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3472

East Asian (EAS) AF: 0.126 AC: 652 AN: 5172

South Asian (SAS) AF: 0.339 AC: 1634 AN: 4816

European-Finnish (FIN) AF: 0.126 AC: 1331 AN: 10592

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9607 AN: 67990

Other (OTH) AF: 0.283 AC: 597 AN: 2108

Alfa AF: 0.0703 Hom.: 95

Bravo AF: 0.321

Asia WGS AF: 0.306 AC: 1065 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	2.8
DANN	Benign	0.47
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs308395; hg19: chr4-123746942;