rs11857532

Positions:

• chr15-78675926-T-G

Variant summary

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

The variant allele was found at a frequency of 0.42 in 152,016 control chromosomes in the GnomAD database, including 13,962 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 0.42 (13962 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78675926T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHRNB4	ENST00000560511.5	n.229-20263A>C		intron_variant		3
ENSG00000290426	ENST00000569846.1	n.366+14392T>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63883 AN: 151898 Hom.: 13951 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.420 AC: 63921 AN: 152016 Hom.: 13962 Cov.: 32 AF XY: 0.411 AC XY: 30509 AN XY: 74298

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.0817

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.409

Alfa AF: 0.438 Hom.: 5707

Bravo AF: 0.419

Asia WGS AF: 0.176 AC: 619 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	3.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11857532; hg19: chr15-78968268;