rs11780486

chr8-8731984-A-G

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, non coding transcript 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: ENST00000522213.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522213.5	n.625-8250T>C		intron_variant, non_coding_transcript_variant		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;