rs3814721

Positions:

• chr11-71998226-C-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 0.831 in 151,888 control chromosomes in the GnomAD database, including 53,904 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 (53904 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.71998226C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126159 AN: 151770 Hom.: 53892 Cov.: 29

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.831 AC: 126212 AN: 151888 Hom.: 53904 Cov.: 29 AF XY: 0.829 AC XY: 61496 AN XY: 74216

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.870

Alfa AF: 0.912 Hom.: 28620

Bravo AF: 0.815

Asia WGS AF: 0.806 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
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: rs3814721; hg19: chr11-71709272;