rs1352864

Positions:

• chr11-27845236-C-A
• chr11-27845236-C-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 0.829 in 152,016 control chromosomes in the GnomAD database, including 52,492 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 0.83 (52492 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.27845236C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000255496	ENST00000530663.1	n.147+32266G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125908 AN: 151898 Hom.: 52452 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.829 AC: 125996 AN: 152016 Hom.: 52492 Cov.: 31 AF XY: 0.830 AC XY: 61700 AN XY: 74310

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.850

Alfa AF: 0.845 Hom.: 112252

Bravo AF: 0.818

Asia WGS AF: 0.733 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1352864; hg19: chr11-27866783;