8-71189916-C-G

Variant names:

• chr8-71189916-C-G
• rs9298162
• ENST00000521685.5:n.271-9224C>G

Variant summary

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

The ENST00000521685.5(ENSG00000254031):​n.271-9224C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,858 control chromosomes in the GnomAD database, including 18,592 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 0.48 (18592 hom., cov: 31)
• Consequence: ENSG00000254031 ENST00000521685.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 2 publications found

Genes affected

ENSG00000254031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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
ENSG00000254031	ENST00000521685.5	n.271-9224C>G		intron_variant	Intron 3 of 5	3
ENSG00000285579	ENST00000647843.1	n.588-9224C>G		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72623 AN: 151740 Hom.: 18565 Cov.: 31

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.479 AC: 72693 AN: 151858 Hom.: 18592 Cov.: 31 AF XY: 0.488 AC XY: 36235 AN XY: 74214

African (AFR) AF: 0.331 AC: 13689 AN: 41382

American (AMR) AF: 0.573 AC: 8752 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1723 AN: 3468

East Asian (EAS) AF: 0.901 AC: 4635 AN: 5142

South Asian (SAS) AF: 0.678 AC: 3254 AN: 4796

European-Finnish (FIN) AF: 0.551 AC: 5826 AN: 10566

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33124 AN: 67932

Other (OTH) AF: 0.489 AC: 1030 AN: 2106

Alfa AF: 0.316 Hom.: 797

Bravo AF: 0.475

Asia WGS AF: 0.758 AC: 2636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.65
DANN	Benign	0.40
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs9298162; hg19: chr8-72102151;