rs11184708

chr1-105887665-A-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 0.114 in 152,146 control chromosomes in the GnomAD database, including 1,122 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 (1122 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 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: 0.114 AC: 17357 AN: 152028 Hom.: 1119 Cov.: 32

Gnomad AFR AF: 0.0904

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.114 AC: 17379 AN: 152146 Hom.: 1122 Cov.: 32 AF XY: 0.117 AC XY: 8674 AN XY: 74366

Gnomad4 AFR AF: 0.0904

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.0885

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.126

Alfa AF: 0.110 Hom.: 116

Bravo AF: 0.115

Asia WGS AF: 0.187 AC: 652 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.90
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11184708; hg19: chr1-106430287;