rs3814758

Positions:

• chr11-119347108-A-G
• chr11-119347108-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 0.589 in 152,032 control chromosomes in the GnomAD database, including 26,504 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 0.59 (26504 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.119347108A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89416 AN: 151912 Hom.: 26475 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.589 AC: 89491 AN: 152032 Hom.: 26504 Cov.: 32 AF XY: 0.591 AC XY: 43933 AN XY: 74304

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.612

Alfa AF: 0.584 Hom.: 3852

Bravo AF: 0.594

Asia WGS AF: 0.718 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3814758; hg19: chr11-119217818;