rs1729410

Variant names:

• chr11-116794945-G-C
• rs1729410

Your query was ambiguous. Multiple possible variants found:

• chr11-116794945-G-C
• chr11-116794945-G-T

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 0.591 in 152,182 control chromosomes in the GnomAD database, including 28,715 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 0.59 (28715 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89751 AN: 152064 Hom.: 28662 Cov.: 33

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.591 AC: 89873 AN: 152182 Hom.: 28715 Cov.: 33 AF XY: 0.596 AC XY: 44331 AN XY: 74386

African (AFR) AF: 0.845 AC: 35111 AN: 41558

American (AMR) AF: 0.590 AC: 9019 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3466

East Asian (EAS) AF: 0.595 AC: 3078 AN: 5174

South Asian (SAS) AF: 0.635 AC: 3071 AN: 4834

European-Finnish (FIN) AF: 0.512 AC: 5410 AN: 10566

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30828 AN: 67978

Other (OTH) AF: 0.559 AC: 1181 AN: 2112

Alfa AF: 0.526 Hom.: 2671

Bravo AF: 0.601

Asia WGS AF: 0.648 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.54
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1729410; hg19: chr11-116665661;