8-91888319-A-G

Variant names:

• chr8-91888319-A-G
• rs1025908
• ENST00000518416.1:n.180+18955T>C

Variant summary

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

The ENST00000518416.1(ENSG00000253901):​n.180+18955T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,154 control chromosomes in the GnomAD database, including 31,647 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 0.63 (31647 hom., cov: 33)
• Consequence: ENSG00000253901 ENST00000518416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 3 publications found

Genes affected

ENSG00000253901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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
ENSG00000253901	ENST00000518416.1	n.180+18955T>C		intron_variant	Intron 1 of 3	4
ENSG00000253901	ENST00000521199.1	n.346+18955T>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.625 AC: 95061 AN: 152034 Hom.: 31602 Cov.: 33

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.625 AC: 95161 AN: 152154 Hom.: 31647 Cov.: 33 AF XY: 0.631 AC XY: 46951 AN XY: 74396

African (AFR) AF: 0.825 AC: 34275 AN: 41542

American (AMR) AF: 0.688 AC: 10511 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2209 AN: 3468

East Asian (EAS) AF: 0.867 AC: 4487 AN: 5178

South Asian (SAS) AF: 0.779 AC: 3759 AN: 4828

European-Finnish (FIN) AF: 0.457 AC: 4832 AN: 10562

Middle Eastern (MID) AF: 0.669 AC: 194 AN: 290

European-Non Finnish (NFE) AF: 0.487 AC: 33109 AN: 67980

Other (OTH) AF: 0.644 AC: 1360 AN: 2112

Alfa AF: 0.505 Hom.: 4211

Bravo AF: 0.647

Asia WGS AF: 0.824 AC: 2863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	15
DANN	Benign	0.63
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs1025908; hg19: chr8-92900547;