rs11780486

Variant names:

• chr8-8731984-A-G
• rs11780486
• ENST00000522213.5:n.625-8250T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522213.5(ENSG00000254367):​n.625-8250T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,166 control chromosomes in the GnomAD database, including 1,584 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 0.12 (1584 hom., cov: 32)
• Consequence: ENSG00000254367 ENST00000522213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.178 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
ENSG00000254367	ENST00000522213.5	n.625-8250T>C		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18772 AN: 152046 Hom.: 1584 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.123 AC: 18773 AN: 152166 Hom.: 1584 Cov.: 32 AF XY: 0.123 AC XY: 9174 AN XY: 74374

Gnomad4 AFR AF: 0.0323

Gnomad4 AMR AF: 0.0891

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0477

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.136

Alfa AF: 0.148 Hom.: 336

Bravo AF: 0.110

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11780486; hg19: chr8-8589494;