11-17719231-C-T

Variant names:

• chr11-17719231-C-T
• rs3911833

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.22 in 152,220 control chromosomes in the GnomAD database, including 4,041 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 0.22 (4041 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33493 AN: 152102 Hom.: 4032 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0247

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.220 AC: 33521 AN: 152220 Hom.: 4041 Cov.: 33 AF XY: 0.216 AC XY: 16071 AN XY: 74430

African (AFR) AF: 0.299 AC: 12414 AN: 41522

American (AMR) AF: 0.200 AC: 3056 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3472

East Asian (EAS) AF: 0.0247 AC: 128 AN: 5176

South Asian (SAS) AF: 0.190 AC: 917 AN: 4822

European-Finnish (FIN) AF: 0.170 AC: 1805 AN: 10608

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13956 AN: 67994

Other (OTH) AF: 0.203 AC: 430 AN: 2114

Alfa AF: 0.199 Hom.: 4042

Bravo AF: 0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.7
DANN	Benign	0.91
PhyloP100		0.44
PromoterAI		0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3911833; hg19: chr11-17740778;