rs3847554

Positions:

• chr11-92935660-C-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 0.551 in 152,056 control chromosomes in the GnomAD database, including 25,967 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 0.55 (25967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83756 AN: 151938 Hom.: 25925 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.551 AC: 83851 AN: 152056 Hom.: 25967 Cov.: 32 AF XY: 0.550 AC XY: 40901 AN XY: 74322

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.531

Alfa AF: 0.437 Hom.: 32430

Bravo AF: 0.557

Asia WGS AF: 0.487 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3847554; hg19: chr11-92668826;