rs11604207

Variant names:

• chr11-77656497-C-T
• rs11604207

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 0.152 in 152,146 control chromosomes in the GnomAD database, including 2,138 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 0.15 (2138 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23139 AN: 152028 Hom.: 2138 Cov.: 31

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.152 AC: 23136 AN: 152146 Hom.: 2138 Cov.: 31 AF XY: 0.148 AC XY: 11033 AN XY: 74374

African (AFR) AF: 0.0520 AC: 2160 AN: 41528

American (AMR) AF: 0.150 AC: 2287 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 751 AN: 3470

East Asian (EAS) AF: 0.0794 AC: 411 AN: 5178

South Asian (SAS) AF: 0.151 AC: 725 AN: 4810

European-Finnish (FIN) AF: 0.165 AC: 1744 AN: 10584

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14460 AN: 67984

Other (OTH) AF: 0.167 AC: 353 AN: 2108

Alfa AF: 0.196 Hom.: 5230

Bravo AF: 0.149

Asia WGS AF: 0.101 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.39
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11604207; hg19: chr11-77367542;