ENST00000670669.1:n.325+108T>G

Variant names:

• chr8-25630477-T-G
• rs4424264
• ENST00000670669.1:n.325+108T>G

Variant summary

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

The ENST00000670669.1(ENSG00000253100):​n.325+108T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,858 control chromosomes in the GnomAD database, including 12,458 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 0.40 (12458 hom., cov: 31)
• Consequence: ENSG00000253100 ENST00000670669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 0 publications found

Genes affected

ENSG00000253100 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670669.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253100	ENST00000670669.1		n.325+108T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60194 AN: 151740 Hom.: 12456 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.397 AC: 60231 AN: 151858 Hom.: 12458 Cov.: 31 AF XY: 0.398 AC XY: 29530 AN XY: 74198

African (AFR) AF: 0.301 AC: 12449 AN: 41424

American (AMR) AF: 0.385 AC: 5874 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1623 AN: 3460

East Asian (EAS) AF: 0.751 AC: 3856 AN: 5132

South Asian (SAS) AF: 0.480 AC: 2306 AN: 4804

European-Finnish (FIN) AF: 0.355 AC: 3741 AN: 10536

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28948 AN: 67940

Other (OTH) AF: 0.425 AC: 895 AN: 2108

Alfa AF: 0.416 Hom.: 20893

Bravo AF: 0.398

Asia WGS AF: 0.605 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.50
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4424264; hg19: chr8-25487993;