rs11163687

Positions:

• chr1-83199436-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;