8-108875310-C-T

Variant names:

• chr8-108875310-C-T
• rs4617129
• ENST00000661381.1:n.441-699G>A

Variant summary

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

The NR_188035.1(LOC101927413):​n.424-699G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,026 control chromosomes in the GnomAD database, including 38,173 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 0.70 (38173 hom., cov: 32)
• Consequence: LOC101927413 NR_188035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 4 publications found

Genes affected

ENSG00000253796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188035.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927413	NR_188035.1		n.424-699G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253796	ENST00000661381.1		n.441-699G>A		intron	N/A
	ENSG00000253796	ENST00000816860.1		n.203-699G>A		intron	N/A
	ENSG00000253796	ENST00000816862.1		n.505-699G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106938 AN: 151908 Hom.: 38120 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.802

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.704 AC: 107049 AN: 152026 Hom.: 38173 Cov.: 32 AF XY: 0.703 AC XY: 52231 AN XY: 74306

African (AFR) AF: 0.807 AC: 33485 AN: 41468

American (AMR) AF: 0.577 AC: 8820 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2687 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3643 AN: 5160

South Asian (SAS) AF: 0.802 AC: 3863 AN: 4814

European-Finnish (FIN) AF: 0.663 AC: 7005 AN: 10566

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45320 AN: 67966

Other (OTH) AF: 0.673 AC: 1417 AN: 2106

Alfa AF: 0.677 Hom.: 137487

Bravo AF: 0.702

Asia WGS AF: 0.783 AC: 2726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.63
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4617129; hg19: chr8-109887539;