11-123055438-C-T

Variant names:

• chr11-123055438-C-T
• rs7111598

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 0.231 in 152,118 control chromosomes in the GnomAD database, including 4,902 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 0.23 (4902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.230 AC: 35018 AN: 152000 Hom.: 4885 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0870

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.231 AC: 35084 AN: 152118 Hom.: 4902 Cov.: 32 AF XY: 0.229 AC XY: 17043 AN XY: 74368

African (AFR) AF: 0.392 AC: 16246 AN: 41474

American (AMR) AF: 0.196 AC: 2988 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3472

East Asian (EAS) AF: 0.0874 AC: 452 AN: 5174

South Asian (SAS) AF: 0.270 AC: 1303 AN: 4824

European-Finnish (FIN) AF: 0.154 AC: 1628 AN: 10592

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11298 AN: 67988

Other (OTH) AF: 0.203 AC: 429 AN: 2114

Alfa AF: 0.197 Hom.: 594

Bravo AF: 0.240

Asia WGS AF: 0.195 AC: 675 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	0.16
DANN	Benign	0.38
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs7111598; hg19: chr11-122926146;