rs1547889

Variant names:

• chr11-68149620-C-T
• rs1547889

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 0.202 in 151,872 control chromosomes in the GnomAD database, including 3,185 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 0.20 (3185 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 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: 0.202 AC: 30725 AN: 151754 Hom.: 3187 Cov.: 30

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.138

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.202 AC: 30734 AN: 151872 Hom.: 3185 Cov.: 30 AF XY: 0.201 AC XY: 14942 AN XY: 74208

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.205

Alfa AF: 0.207 Hom.: 3375

Bravo AF: 0.195

Asia WGS AF: 0.191 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547889; hg19: chr11-67917087;