chr8-82520833-G-A

Variant names:

• chr8-82520833-G-A
• rs11783821
• ENST00000522776.5:n.450+2400C>T

Variant summary

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

The ENST00000522776.5(ENSG00000253503):​n.450+2400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,050 control chromosomes in the GnomAD database, including 3,831 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 0.21 (3831 hom., cov: 32)
• Consequence: ENSG00000253503 ENST00000522776.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 1 publications found

Genes affected

ENSG00000253503 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375931	XR_929115.3	n.321+32560G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253503	ENST00000522776.5	n.450+2400C>T		intron_variant	Intron 6 of 6	4
ENSG00000254394	ENST00000658531.1	n.149+32560G>A		intron_variant	Intron 2 of 3
ENSG00000254394	ENST00000659043.1	n.387-19083G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31331 AN: 151932 Hom.: 3826 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.206 AC: 31358 AN: 152050 Hom.: 3831 Cov.: 32 AF XY: 0.206 AC XY: 15277 AN XY: 74324

African (AFR) AF: 0.322 AC: 13365 AN: 41450

American (AMR) AF: 0.266 AC: 4066 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3472

East Asian (EAS) AF: 0.286 AC: 1473 AN: 5158

South Asian (SAS) AF: 0.151 AC: 724 AN: 4808

European-Finnish (FIN) AF: 0.124 AC: 1307 AN: 10570

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9179 AN: 68002

Other (OTH) AF: 0.213 AC: 448 AN: 2108

Alfa AF: 0.104 Hom.: 243

Bravo AF: 0.225

Asia WGS AF: 0.226 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs11783821; hg19: chr8-83433068;