chr11-125438180-G-C

Position:

• chr11-125438180-G-C

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 0.269 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.269 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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.272

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1615640; hg19: chr11-125308076;