rs2727789

Variant names:

• chr11-116826171-G-T
• rs2727789

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 0.531 in 152,106 control chromosomes in the GnomAD database, including 22,755 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 0.53 (22755 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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: 0.531 AC: 80727 AN: 151988 Hom.: 22754 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.531 AC: 80750 AN: 152106 Hom.: 22755 Cov.: 33 AF XY: 0.526 AC XY: 39109 AN XY: 74340

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.557

Alfa AF: 0.574 Hom.: 3520

Bravo AF: 0.529

Asia WGS AF: 0.540 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2727789; hg19: chr11-116696887;