rs1365406

chr11-12541173-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 0.587 in 152,182 control chromosomes in the GnomAD database, including 26,586 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 (26586 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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: 0.587 AC: 89263 AN: 152064 Hom.: 26557 Cov.: 35

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.587 AC: 89336 AN: 152182 Hom.: 26586 Cov.: 35 AF XY: 0.580 AC XY: 43122 AN XY: 74374

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.573

Alfa AF: 0.584 Hom.: 43354

Bravo AF: 0.579

Asia WGS AF: 0.497 AC: 1727 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	13
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1365406; hg19: chr11-12562720;