rs3897566

Variant names:

• chr11-128947505-C-T
• rs3897566

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.201 AC: 8335 AN: 41508

American (AMR) AF: 0.118 AC: 1801 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3472

East Asian (EAS) AF: 0.118 AC: 613 AN: 5178

South Asian (SAS) AF: 0.139 AC: 669 AN: 4812

European-Finnish (FIN) AF: 0.269 AC: 2844 AN: 10578

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14720 AN: 67986

Other (OTH) AF: 0.155 AC: 327 AN: 2112

Alfa AF: 0.200 Hom.: 5930

Bravo AF: 0.185

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs3897566; hg19: chr11-128817400;