rs1554338

chr11-45885279-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 0.14 in 152,124 control chromosomes in the GnomAD database, including 2,407 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 0.14 (2407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 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: 0.140 AC: 21224 AN: 152006 Hom.: 2406 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0878

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0346

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.140 AC: 21279 AN: 152124 Hom.: 2407 Cov.: 32 AF XY: 0.138 AC XY: 10252 AN XY: 74378

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0880

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0346

Gnomad4 NFE AF: 0.0606

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0813 Hom.: 1062

Bravo AF: 0.155

Asia WGS AF: 0.157 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.9
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: rs1554338; hg19: chr11-45906830;