chr11-71998226-C-T

Variant names:

• chr11-71998226-C-T
• rs3814721

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;