rs877138

Variant names:

• chr11-113385786-G-A
• rs877138

Your query was ambiguous. Multiple possible variants found:

• chr11-113385786-G-A
• chr11-113385786-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 0.68 in 152,144 control chromosomes in the GnomAD database, including 35,606 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 0.68 (35606 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103390 AN: 152026 Hom.: 35586 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.680 AC: 103457 AN: 152144 Hom.: 35606 Cov.: 33 AF XY: 0.676 AC XY: 50266 AN XY: 74358

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.681

Alfa AF: 0.664 Hom.: 44874

Bravo AF: 0.677

Asia WGS AF: 0.555 AC: 1927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs877138; hg19: chr11-113256508;