rs1554338

Variant names:

• chr11-45885279-A-G
• rs1554338

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;