rs11708304

Positions:

• chr3-133542030-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 0.112 in 151,962 control chromosomes in the GnomAD database, including 1,207 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 0.11 (1207 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16953 AN: 151844 Hom.: 1205 Cov.: 31

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0718

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.112 AC: 16954 AN: 151962 Hom.: 1207 Cov.: 31 AF XY: 0.112 AC XY: 8288 AN XY: 74286

Gnomad4 AFR AF: 0.0272

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0719

Gnomad4 SAS AF: 0.0503

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.114

Alfa AF: 0.132 Hom.: 208

Bravo AF: 0.103

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.2
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11708304; hg19: chr3-133260874;