rs11264329

Positions:

• chr1-155122682-A-G
• chr1-155122682-A-T

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 0.569 in 152,062 control chromosomes in the GnomAD database, including 26,081 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 0.57 (26081 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.155122682A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86422 AN: 151944 Hom.: 26066 Cov.: 31

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.569 AC: 86478 AN: 152062 Hom.: 26081 Cov.: 31 AF XY: 0.566 AC XY: 42088 AN XY: 74328

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.525

Alfa AF: 0.472 Hom.: 24342

Bravo AF: 0.591

Asia WGS AF: 0.676 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11264329; hg19: chr1-155095158;