ENST00000668834.2:n.372+18553A>G

Variant names:

• chr8-74184756-A-G
• rs4385459
• ENST00000668834.2:n.372+18553A>G

Variant summary

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

The ENST00000668834.2(ENSG00000254288):​n.372+18553A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,948 control chromosomes in the GnomAD database, including 24,940 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 0.57 (24940 hom., cov: 32)
• Consequence: ENSG00000254288 ENST00000668834.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900
• Publications: 2 publications found

Genes affected

ENSG00000254288 (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 = 0.624 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
ENSG00000254288	ENST00000668834.2	n.372+18553A>G		intron_variant	Intron 2 of 2
ENSG00000254288	ENST00000670556.2	n.464+18553A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86341 AN: 151830 Hom.: 24921 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.569 AC: 86418 AN: 151948 Hom.: 24940 Cov.: 32 AF XY: 0.574 AC XY: 42596 AN XY: 74256

African (AFR) AF: 0.630 AC: 26107 AN: 41424

American (AMR) AF: 0.577 AC: 8814 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1905 AN: 3466

East Asian (EAS) AF: 0.435 AC: 2240 AN: 5152

South Asian (SAS) AF: 0.421 AC: 2027 AN: 4810

European-Finnish (FIN) AF: 0.691 AC: 7305 AN: 10564

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36255 AN: 67940

Other (OTH) AF: 0.543 AC: 1148 AN: 2116

Alfa AF: 0.537 Hom.: 36613

Bravo AF: 0.564

Asia WGS AF: 0.436 AC: 1515 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	0.33
DANN	Benign	0.65
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs4385459; hg19: chr8-75096991;