rs11163687

Variant names:

• chr1-83199436-A-G
• rs11163687

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 0.097 in 152,238 control chromosomes in the GnomAD database, including 913 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 0.097 (913 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.155 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: 0.0971 AC: 14765 AN: 152120 Hom.: 911 Cov.: 32

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0575

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0970 AC: 14768 AN: 152238 Hom.: 913 Cov.: 32 AF XY: 0.0948 AC XY: 7055 AN XY: 74448

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.0579

Gnomad4 SAS AF: 0.0998

Gnomad4 FIN AF: 0.0845

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.116 Hom.: 383

Bravo AF: 0.101

Asia WGS AF: 0.0880 AC: 305 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.6
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11163687; hg19: chr1-83665119;