rs3934007

Positions:

• chr11-113668358-A-G
• chr11-113668358-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 0.632 in 151,996 control chromosomes in the GnomAD database, including 31,061 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 0.63 (31061 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113668358A>G		intergenic_region
LOC107984390	XR_001748390.2	n.5178+12975T>C		intron_variant
LOC107984390	XR_001748391.2	n.5178+12975T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95892 AN: 151878 Hom.: 31002 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.632 AC: 96012 AN: 151996 Hom.: 31061 Cov.: 32 AF XY: 0.627 AC XY: 46579 AN XY: 74310

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.608

Alfa AF: 0.581 Hom.: 52281

Bravo AF: 0.654

Asia WGS AF: 0.606 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3934007; hg19: chr11-113539080;