chr11-125438180-G-C

Variant names:

• chr11-125438180-G-C
• rs1615640

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 0.269 in 152,046 control chromosomes in the GnomAD database, including 6,190 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 0.27 (6190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.385 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: 0.269 AC: 40871 AN: 151928 Hom.: 6190 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.269 AC: 40871 AN: 152046 Hom.: 6190 Cov.: 32 AF XY: 0.275 AC XY: 20462 AN XY: 74314

African (AFR) AF: 0.133 AC: 5532 AN: 41478

American (AMR) AF: 0.394 AC: 6011 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3468

East Asian (EAS) AF: 0.384 AC: 1987 AN: 5176

South Asian (SAS) AF: 0.244 AC: 1174 AN: 4814

European-Finnish (FIN) AF: 0.385 AC: 4069 AN: 10570

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20052 AN: 67958

Other (OTH) AF: 0.272 AC: 573 AN: 2108

Alfa AF: 0.279 Hom.: 803

Bravo AF: 0.266

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	19
DANN	Benign	0.53
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1615640; hg19: chr11-125308076;