rs922501

Variant names:

• chr8-2228332-C-A
• rs922501
• ENST00000776947.1:n.299-208C>A

Variant summary

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

The ENST00000776947.1(ENSG00000288782):​n.299-208C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,836 control chromosomes in the GnomAD database, including 7,574 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 0.30 (7574 hom., cov: 32)
• Consequence: ENSG00000288782 ENST00000776947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 0 publications found

Genes affected

ENSG00000288782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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
ENSG00000288782	ENST00000776947.1	n.299-208C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44852 AN: 151720 Hom.: 7558 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.296 AC: 44917 AN: 151836 Hom.: 7574 Cov.: 32 AF XY: 0.286 AC XY: 21243 AN XY: 74194

African (AFR) AF: 0.448 AC: 18524 AN: 41366

American (AMR) AF: 0.204 AC: 3114 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3460

East Asian (EAS) AF: 0.0780 AC: 403 AN: 5166

South Asian (SAS) AF: 0.174 AC: 838 AN: 4814

European-Finnish (FIN) AF: 0.182 AC: 1919 AN: 10538

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18365 AN: 67900

Other (OTH) AF: 0.289 AC: 609 AN: 2110

Alfa AF: 0.310 Hom.: 830

Bravo AF: 0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs922501; hg19: chr8-2176000;