rs11711286

Variant names:

• chr3-37985161-C-T
• rs11711286

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 0.192 in 152,114 control chromosomes in the GnomAD database, including 3,104 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 0.19 (3104 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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: 0.192 AC: 29111 AN: 151996 Hom.: 3101 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.192 AC: 29144 AN: 152114 Hom.: 3104 Cov.: 33 AF XY: 0.189 AC XY: 14053 AN XY: 74368

African (AFR) AF: 0.274 AC: 11381 AN: 41484

American (AMR) AF: 0.119 AC: 1814 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 422 AN: 3468

East Asian (EAS) AF: 0.0866 AC: 448 AN: 5172

South Asian (SAS) AF: 0.273 AC: 1318 AN: 4820

European-Finnish (FIN) AF: 0.124 AC: 1312 AN: 10588

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.176 AC: 11940 AN: 67980

Other (OTH) AF: 0.164 AC: 346 AN: 2104

Alfa AF: 0.175 Hom.: 4251

Bravo AF: 0.193

Asia WGS AF: 0.175 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.78
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs11711286; hg19: chr3-38026652;