rs3897566

Variant names:

• chr11-128947505-C-T
• rs3897566

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 0.198 in 152,142 control chromosomes in the GnomAD database, including 3,089 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 (3089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 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: 0.198 AC: 30074 AN: 152024 Hom.: 3090 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.198 AC: 30080 AN: 152142 Hom.: 3089 Cov.: 32 AF XY: 0.199 AC XY: 14776 AN XY: 74374

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.155

Alfa AF: 0.203 Hom.: 4432

Bravo AF: 0.185

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3897566; hg19: chr11-128817400;