11-86103988-G-A

Variant names:

• chr11-86103988-G-A
• rs1237999

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 0.693 in 152,120 control chromosomes in the GnomAD database, including 37,146 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 0.69 (37146 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105389 AN: 152002 Hom.: 37112 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.693 AC: 105479 AN: 152120 Hom.: 37146 Cov.: 32 AF XY: 0.688 AC XY: 51178 AN XY: 74350

African (AFR) AF: 0.833 AC: 34604 AN: 41532

American (AMR) AF: 0.641 AC: 9802 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2142 AN: 3470

East Asian (EAS) AF: 0.595 AC: 3076 AN: 5174

South Asian (SAS) AF: 0.566 AC: 2731 AN: 4822

European-Finnish (FIN) AF: 0.636 AC: 6721 AN: 10564

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44237 AN: 67956

Other (OTH) AF: 0.685 AC: 1450 AN: 2116

Alfa AF: 0.661 Hom.: 55391

Bravo AF: 0.700

Asia WGS AF: 0.590 AC: 2053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1237999; hg19: chr11-85815030;