rs3824088

Variant names:

• chr8-81448894-A-G
• rs3824088
• ENST00000524085.2:n.298+8801A>G

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.298+8801A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,218 control chromosomes in the GnomAD database, including 2,867 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 0.16 (2867 hom., cov: 32)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 4 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 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
ENSG00000253374	ENST00000524085.2	n.298+8801A>G		intron_variant	Intron 2 of 3	5
ENSG00000253374	ENST00000832857.1	n.326+8801A>G		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.308+8801A>G		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.327+8801A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24105 AN: 152100 Hom.: 2866 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0934

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.159 AC: 24134 AN: 152218 Hom.: 2867 Cov.: 32 AF XY: 0.157 AC XY: 11685 AN XY: 74436

African (AFR) AF: 0.248 AC: 10300 AN: 41518

American (AMR) AF: 0.168 AC: 2571 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3470

East Asian (EAS) AF: 0.606 AC: 3134 AN: 5170

South Asian (SAS) AF: 0.102 AC: 495 AN: 4834

European-Finnish (FIN) AF: 0.0570 AC: 605 AN: 10614

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0934 AC: 6349 AN: 67998

Other (OTH) AF: 0.156 AC: 329 AN: 2114

Alfa AF: 0.120 Hom.: 6893

Bravo AF: 0.177

Asia WGS AF: 0.334 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.60
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs3824088; hg19: chr8-82361129;