rs1729408

Variant names:

• chr11-116804102-A-G
• rs1729408

Your query was ambiguous. Multiple possible variants found:

• chr11-116804102-A-G
• chr11-116804102-A-T

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 0.475 in 152,086 control chromosomes in the GnomAD database, including 20,189 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 0.48 (20189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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: 0.475 AC: 72204 AN: 151968 Hom.: 20150 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.475 AC: 72302 AN: 152086 Hom.: 20189 Cov.: 32 AF XY: 0.472 AC XY: 35088 AN XY: 74346

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.431

Alfa AF: 0.355 Hom.: 9536

Bravo AF: 0.492

Asia WGS AF: 0.433 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1729408; hg19: chr11-116674818;