chr5-4198709-A-G

Variant names:

• chr5-4198709-A-G
• rs6882308
• ENST00000762810.1:n.*95A>G

Variant summary

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

The ENST00000762810.1(ENSG00000299354):​n.*95A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,262 control chromosomes in the GnomAD database, including 68,723 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 0.95 (68723 hom., cov: 33)
• Consequence: ENSG00000299354 ENST00000762810.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 2 publications found

Genes affected

ENSG00000299354 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762810.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299354	ENST00000762810.1		n.*95A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144493 AN: 152144 Hom.: 68674 Cov.: 33

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.964

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.950 AC: 144596 AN: 152262 Hom.: 68723 Cov.: 33 AF XY: 0.950 AC XY: 70743 AN XY: 74430

African (AFR) AF: 0.924 AC: 38374 AN: 41546

American (AMR) AF: 0.964 AC: 14749 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3361 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5133 AN: 5162

South Asian (SAS) AF: 0.906 AC: 4367 AN: 4820

European-Finnish (FIN) AF: 0.985 AC: 10449 AN: 10610

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65027 AN: 68038

Other (OTH) AF: 0.936 AC: 1980 AN: 2116

Alfa AF: 0.952 Hom.: 12751

Bravo AF: 0.949

Asia WGS AF: 0.920 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.42
DANN	Benign	0.26
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs6882308; hg19: chr5-4198822;